X-ray Crystallography Technique Analysis

X-ray Crystallography Technique Analysis1 Limitations of roentgenogram watch watch quartzlographyFrom the first liquid body structure determination of table salt in 1914 whose structure elucidation proved the existence of ionic mingleds (6), bingle crystal roentgen ray diffraction (SC-XRD) has been widening our view of the hidden world of molecular structures. Today, SC-XRD continues to be the alone structural synopsis method that offers direct structural breeding at the atomic level. As such, this proficiency has been vital for reliably firmness of purpose many structures of small molecules such as neurotransmitters, antibiotics and industrial catalysts.SC-XRD utilises the ability of gauzy atoms to scatter or diffract a publicize of incident x-ray into a series of amplified and spatially constrained beams (3). The angles and intensities of these beams can be measured and computationally edgeed by a crystallographer to produce a 3-dimensional visualize of the density of electrons in the crystal. Aside from the expertise requisite to process the reflectance info produced, the fundamental requirement of crystals for this technique acts as major bound, since single molecules scatter the incident x-ray to produce a weak, continuous beam that provides shrimpy wontful in induceation for analysis. While technological advances in new-made decades including senior high schoolly intense x-ray beams produced by synchrotrons and the development of more the right way algorithms for molecular structure imaging have allowed the size of the crystal take to be increasingly smaller, the need for a crystal has settle down non been eliminated. This poses a great issue as many orchestrate compounds argon very difficult to crystallise, thus requiring experienced specialists bit others will lonesome(prenominal) when not crystallise at all. In 2013, a new protocol, subsequent coined the pellucid sponger method (CSM), was in chance variable that at tempted to bypasses this intrinsic limitation of the design molecule needing to be coherent (1).2 The journey of the crystalline sponge methodExpectationsFujita and his squad described the new method that promised to renovate up SC-XRD drastically by eliminating the crystallization smell of the target molecule. This was through using porous metal ingrained frameworks (MOFs) that act as crystalline sponges. Due to the high molecular recognition capability of their pores, these sponges can take target molecules from the hear solution into their pores. In their study, Fujita and his team used dickens MOFs synthesised from tris(4-pyridyl)-1,3,5-triazine (TTP, 1) and the appropriate metal salt as their crystalline sponges (Co(NCS)2)3(TTP)4x( reply)n (2) and (ZnI2)3(TTP)2x( issue)n (3). In both conglomeratees, the void spaces showed strong spine properties for incoming lymph node molecules do them ideal crystalline sponges. The as-synthesized complexes2 and 3 have goted res olutions in the void. By soaking the crystals of 2 and 3 in a node solution, knob molecules abately penetrate these wet cavities by lymph node exchange, and are strong at the molecular-recognition pockets surrounded by TTP. A characteristic of the strong troops-guest fundamental interaction in the crystals of 2 and 3 lies in panel ligand1, which attracts various guests onto its electron-deficient -plane. The slow guest exchange allows for the process to remain under thermodynamic control, comment the geometry of the included guests to be regularly ordered and well(p) equilibrated, thus making it possible to analyse the accommo epochd guests by crystallography since the molecular structure of the take up guest will be displayed, along with the host framework.Since theoretically, only one crystal is needed to perform the experiment, Fujitas team tack together that even trace sample amounts of the microgram-nanogram scale can be analysed in this protocol. When the team used o nly 80ng of guaiazulene guest sample with a crystal of 3 (80-80-80m3), they were surprised to see the guestwas still understandably observed. Considering that the experiment was carried out using a laboratory X-ray machine, it seemed shiny to accomplish crystallography with synchrotron X-ray experiments even on a mass of In order to assess the scope of the method, the team carried out blind crystallographic analysis of six appropriate samples (Fig) with only 5g of each sample. In conjunction with mass spectroscopic data, all six structures were correctly assigned, with triosome of the structures solved solely from the crystallographic data. Additionally, the protocol was success in fully used to determine the exacting stereochemistry of santonin 4, an anthelminthic drug bearing four chiral centres. Unlike common inviolable structure determinations, this was achieved without the chemical introduction of heavy atoms on the guest framing since the host framework contains heavy at oms (Zn and I) that show enhanced anomalous dissipate effects. (ExpandThe most impressive result of the teams protocol however was determining the unquestioning structure of miyakosyneA 5, a scarce natural marine harvest-tide tardily isolated from a marine sponge Petrosia sp. The structure contains three chiral centres on its main alkyl chain, two of which, C3 and C26, had been previously determined to be 3R and 26R respectively. However, since the difference between the two long alkyl groups on C14 is only one methylene unit, determining the absolute configuration at C14 was tooth slight by conventional spectroscopic and chemical methods. As the amount of miyakosyneA was very limited, education a single crystal for X-ray crystallography would propose a huge challenge. The team were able apply their method to the full characterization of miyakosyneA to determine the absolute configuration at C14 and inform success. For its appraisers, it was this result that made this new pro tocol transformational (4) and understandably it led to a lot of excitement in the field.1.3 The FallThe initial lustre of the protocol was dulled as Fujita and his team published a correction on the initial report later that year (1b). Previously unnoticed ambiguities in the crystallographic data, alongside further investigation of by the team found the initial assignment of stereochemistry at C14 of 5 to have been incorrect. Synthetic studies by the team determined the methyls stereochemistry was opposite to the original assignment reported. Poor data attribute was concluded to be the cause of this errors.Additionally, more problems were met as other question groups tried to use the technique in their own labs. Although success with the technique was achieved for simple molecules, in the first few months, other groups found little success with any interesting structures, particularly large molecules or molecules containing alkaline chemical groups (8b). Fujitas team were able to aid other industrial and academician groups to master the technique in one to two weeks. Additionally, more of the issues in reproducibility were improved by the release of a more lucubrate report of the method (1c) that described the sponge synthesis, pore- upshot exchange and selection requirements for high quality single crystals for crystallography. However, this did not address the issue of poor data quality that led to the misassignment of 5. Since poor data quality can be attributed to all steps of the CSM, including cystal synthesis, resoluteness exchange, guest-soaking, data collection and crystallographic refinement of the host-guest complex molecules in order to move the CSM from the fascinating idea phase into sightly the transformational and reliable new technology it was envisioned to be, more work was required to optimise all these steps.3. (ZnI2)3(TTP)2x(solvent)n The most successful sponge to date3.1 Andvantages of (ZnI2)3(1)2x(solvent)nIn their initial paper, Fujita and his team reported using sponges 2 and 3. With further investigation, in the case of complex 2, it was observed that guest molecules absorbed in the sponge were prone to static disorder as they tip to lay on the symmetry elements of the cubic lattice (Fm3m). Additionally, complex 2 was shown to undergo unfavourable transformations when removed from solution (8c). This destabilising transformation, accompanied by a colour change from orange to green, resulted in a semiamorphous solid with a significantly altered coordination environment at the metal centre. As such, the less symmetric (C2/c) complex 3 has been employed as the primary host complex for the crystalline sponge. The versatility of 3 as a crystal sponge stems from several advantages in host-guest complexation in the pores. Firstly, the size of the pores is ideal for accommodating organic molecules of common sizes, while the hydrophobic nature of the pore cavities provides favourable screen of common organic mo lecules. Also, ligand 1 in the complex offers flat and electron-deficient concealment site, appropriate for stacking with aromatic compounds and for CH- interactions even with aliphatic compounds (9). Since the I atoms in the ZnI2 are good hydrogen-bond acceptors and the pyridyl protons of the ligand 1 are good hydrogen-bond donors, they provide efficient binding sites through hydrogen-bonding. Finally, the framework of sponge 3 is reatively flexible with the size of the guest not strictly limited to the pore size of the complex. Molecules larger than the adit are often accommodated by expanding the pore size. (1.3)3.2.1 Synthesis of (ZnI2)3(1)2x(solvent)n and solvent exchange by Fujita method and updated Clardy methodIn their investigations, Fujita and co-workers prepared 3 by layering a solution of zinc iodide in methanol onto a denser solution of TTP (1) in nitrobenzene. The solution is allowed to stand for 7 days, over which crystals form at the boundary of the two solvents as they diffuse before drop to the bottom of the test tube and being isolated by filtration. The as-synthesised crystals contain nitrobenzene molecules in the void spaces. However, since nitrobenzene has a high affinity to the pores, target guests are poorly absorbed into the as-synthesised crystal. As such, a solvent exchange step that replaces nitrobenzene with an inert, noninteractive solvent is required prior to soaking the crystal in the target guest solution.Cyclohexane can be adopted as the inert solvent, while pentane also proves useful for guest soaking at temperatures below 0oC. The solvent exchange step is carried out by soaking the crystal in the inert solvent for 7 days at 50oC. The success of the process can be monitered throughout by observing the disappearance of the indication at 1346 cm-1 in an Infrared (IR) spectrum, which can be assigned to nitrobenzene. uttermost of the process is confirmed by SC-XRD by the presence of ordered cyclohexane molecules in the pores . The sponge whitethorn now be used for guest absorption. This solvent exchange process may complicate the refinement of the structure, since some nitrobenzene may reamin within the sponge structure after exchange (Vinogradova et al., 2014). This becomes an issue if the target guest molecule contains cyclohexyl or aromatic rings, as it may be difficult to distinguish the guest from quietus solvent, especially if the site line is low or the data quality is poor. Accompanied with heavy use of crystallographic restraints, this increases the risk of misassignment of the desired guest molecule by using residual solvent electron density. Additionally, if the residual solvent and the guest interact withal with the host, the likelihood of occupational disorder increases and making structure refinement much more challenging.Clardy and co-workers later reported a simpler and less timely preparation method for the synthesis of sponge 3 using similar conditions to those reported by Fujita an d his team. (5sync) Instead of conducting the layer diffusion step with TTP in nitrobenzene, TTP is dissolve in chloroform. As such, the as-synthesised crystals of sponge 3 contain chloroform in the pores. Since chloroform has a much lower affinity for the solvent pores than nitrobenzene, the solvent exchange step can be omitted and the as-synthesised crystals used immediately. As well as saving 7 days of preparation by omitting the solvent exchange step, this method is also milder as it does not require the crystal to be heated for long periods of time. This reduces the chances of introducing imperfections in the crystal.This omission also minimises the turning of solvents that the crystal is exposed to, reducing issues in structure refinement. Although some CHCl3 mightiness remain within the sponge after guest inclusion, due to its chronic C-Cl bond length (1.7) and larger Cl electron density, CHCl3 can still be observed. This greater electron density for CHCl3 exerts a larger square off on the structure factors relative to incorporated guest compared to nitrobenzene, however the benefits of CHCl3 physical exercise override this issue.In addition to the desired crystals, this preparation method has been found to simultaneously form other crystalline structures. Firstly, a crystalline compound with the formula (ZnI2)3(TPT)2CHCl3n (2), having a much smaller pore size has been viewed. Fortunately, this crystalline structure can be easily distinguished from the desired structure from its syllable structure (Fig). A second undesired crystal has more recently been observed with consistently distinct unit parameter, but having indistinguishable morphology to the desired structure from its morphology (Fig). Both these crystals are believed to form due to slight changes in humidity and temperature as well as variations in mixing in the initial stages of the layering process. desired crystal. Both these crystals are believed to form due to slight changes in humi dity and temperature as well as variations in mixing in the initial stages of the layering process.