Cool Structures: Important Science from Small Molecules

Conference: 2020: 70th ACA Annual Meeting
08/07/2020: 12:00 PM  - 3:00 PM 
Oral Session 


This session aims to both highlight interesting structures of small molecules (<100 atoms per molecule) and bring to the foreground the science enabled by small-molecule structure analysis. Speakers will be selected from contributed abstracts. Submissions from students are encouraged.


Exploring Twinning in the CSD

12:00 PM - 12:20 PM 
The 2020 Version 5.41 (November 2019) of the Cambridge Structural Database1 now boasts 1,000,000-plus crystal structures of organic, organometallic, and other related materials containing organic molecular fragments. Of these, 19,156 are cited as being twins of some sort. Quite often the type of twin is omitted from the description altogether. We have embarked on a detailed study of this group of crystal structures to learn various hidden details of interest. First of all, while the descriptor twin is often listed, we often find the respective authors determined experimentally that specimen to be a single crystal (actual inversion twin by use of the Flack X parameter) within accepted standard uncertainties. On the other hand, the absence of modifiers; e.g. inversion, merohedral, non-merohedral, and recticular; reduces the overall value to the database and the additional research opportunities it could provide. The present study will focus on crystal structures within the triclinic crystal system where twin is indicated or where some sort of twin should be indicated. The vast majority of these are Z'>1 crystal structures. Our study will also focus on two major subgroups, transformational- and growth twins, in order to learn more about their composition planes and putative, unexplored/unreported enantiotropic phase transitions. Several useful software tools will be presented in use with worked examples. 1. The Cambridge Structural Database, C. R. Groom, I. J. Bruno, M. P. Lightfoot and S. C. Ward, Acta Cryst. (2016). B72, 171-179 DOI: 10.1107/S2052520616003954 

View Abstract 150


Victor Young, Dept of Chemistry, Univ of Minnesota Minneapolis, MN 

Additional Author

Bruce Foxman, Chemistry MS015, Brandeis Univ

Understanding the stoichiometric diversity and reactions of cocrystals through experimental and computational studies

12:20 PM - 12:40 PM 
Halogen bonding, a weak interaction formed between the electropositive areas of halogen atoms as donors and electron rich atoms and moieties as acceptors, has in the last two decades been established as a useful addition to the toolbox of supramolecular interactions, conceptually similar yet very different from hydrogen bonding. During this time, solid-state has emerged as the critical medium for the studies of halogen bonding, with crystallography as the most important tool. Cocrystallization in particular has enabled easy access to a large number of systems where the influence of a range of donors and acceptors on the halogen bond properties can be studied. Using di- or multi-topic halogen bond donors and acceptors opens the possibility of obtaining cocrystals comprising same components in different stoichiometric ratios – [i]stoichiomorphs[/i], as not all donor/acceptor sites will necessarily engage in halogen bonding. Moreover, other interactions, such as weak hydrogen bonds involving C−H donors and aromatic ring stacking can also more or less successfully compete with the halogen bonding. Outcomes of such cocrystallization reactions can often be tuned by adjusting the stoichiometric ratio of the coformers. In addition to stoichiomorphism, polymorphism can also complicate the structural landscape of even a very simple halogen-bonded cocrystal system.[sup]1[/sup] Mechanochemistry has been demonstrated to be a highly efficient and rapid screening method for the formation of molecular solids such as cocrystals.[sup]2[/sup] Bypassing potential solubility issues,[sup]3[/sup] it allows for easy stoichiometric control, as two or more coformer solids can be directly transformed into the novel cocrystalline form.[sup]2[/sup] Furthermore, interconversion between cocrystals of different stoichiometries can be easily achieved mechanochemically, by adding a small amount of the respective coformer and grinding.[sup]2,4[/sup] Such transformations can also be followed both [i]in situ[/i] and [i]ex situ[/i] by a range of diffraction and spectroscopic techniques. In our work, we focused on a small set of bromine- or iodine-based halogen bond donors and nitrogen-based acceptors. Their cocrystallization was studied by neat or liquid-assisted grinding, and the milling times and stoichiometric ratios of donors and acceptors were varied. Phase analysis was conducted by powder X-ray diffraction, with the structure analysis performed by single-crystal X-ray diffraction. Finally, state-of-the-art periodic DFT calculations were used to establish the relative stabilities of different phases.[sup]1,4–6[/sup] We found that the stoichiometry of the cocrystals formed in mechanochemical cocrystallization reactions is reliably determined by the starting stoichiometric ratio of the coformers. However, through ex situ analysis, we observed the formation of different stoichiometric variants and polymorphs as the intermediates during cocrystallization. We also used periodic DFT calculations to predict the possibility of interconversion of different stoichiometric variants, which was subsequently confirmed experimentally. References 1 F. Topić [i]et al.[/i], [i]Chem. Commun.[/i], 2019, [b]55[/b], 14066–14069. 2 S. Karki, T. Friščić and W. Jones, [i]CrystEngComm[/i], 2009, [b]11[/b], 470–481. 3 T. Friščić [i]et al.[/i], [i]CrystEngComm[/i], 2009, [b]11[/b], 418–426. 4 M. Arhangelskis [i]et al.[/i], [i]Chem. Commun.[/i], DOI: 10.1039/D0CC02935A. 5 K. Lisac [i]et al.[/i], [i]Cryst. Growth Des.[/i], 2018, [b]18[/b], 2387–2396. 6 K. Lisac [i]et al.[/i], [i]Nat. Commun.[/i], 2019, [b]10[/b], 61. 

View Abstract 313


Filip Topic Montreal

Additional Author(s)

Mihails Arhangelskis, University of Warsaw Warsaw
Poppy Hindle, McGill University Montreal, Quebec 
Ricky Tran, McGill University Montreal, Quebec 
Andrew J. Morris, University of Birmingham Birmingham
Tomislav Friscic, McGill University

Uranyl Dicyanoaurate Coordination Polymers Through the Dimensions

12:40 PM - 1:00 PM 
The structural chemistry of uranyl (UO[sub]2[/sub][sup]+2[/sup]) coordination polymer chemistry has been greatly expanded by recent work, but it currently remains dominated by bridging units bearing carboxylic acids. To expand this field, we have used dicyanoaurate (Au(CN)[sub]2[/sub][sup]-[/sup] ) linkers in the creation of coordination polymers. Initial efforts showed an interesting array of one-dimensional coordination polymers, and we have recently completed work expanding these structures to be multidimensional using aurophilic interactions and hydrogen bonds. 

View Abstract 184


Matthew Brown, Simon Fraser University Burnaby, BC 

Coffee Break

1:00 PM - 1:20 PM 

Cool structures from event-based single crystal neutron diffraction

1:20 PM - 1:40 PM 
Neutron diffraction is sensitive to the nuclear density of atoms. Isotopes of the same element can have very different neutron scattering properties; for example, the scattering length is negative for hydrogen and positive for deuterium. Unlike X-rays form factors, neutron scattering lengths do not decrease for high Q reflections, advantageous for using neutron diffraction to locate light elements at the subatomic resolution, including hydrogen positions for the study of hydrogen bonding interactions. Neutron wavelength‐resolved time-of-flight Laue technique expands the measured diffraction pattern from 2D on detector spaces to wavelength‐resolved 3D volume in (x, y, λ) along the neutron transport direction. Neutron event data collection at Spallation Neutron Source uses an array of area detectors on TOPAZ with a fast detection time in the microsecond scale. A large number of reflections can be measured at one sample orientation. Metadata with 'real-time' parameter information are saved with event data, ideal for the study of temporal and stroboscopic structural changes induced by external stimuli such as temperature, pressure, electric and magnetic fields. We have used the TOPAZ instrument to locate hydrides and deuterium atoms in transition metal complexes, study the phase transition and temperature dependence of hydrogen bonding in hybrid organic-inorganic perovskites (HOIPs) by collecting the 3D volume of diffraction patterns in neutron event mode. Variable temperature data from single-crystal neutron diffraction following the initiation of orthorhombic-tetragonal phase transition provided details for the change of hydrogen bonding pattern between the organic donor and the inorganic accepter in HOIP compounds. The corresponding neutron structures and hydrogen bonding interactions will be presented. 

View Abstract 341


Xiaoping Wang, Oak Ridge National Laboratory Oak Ridge, TN 

Utilizing Single-Crystal X-ray Diffraction to Determine Unusual Structural Trends within Group 15 Triamido Complexes

1:40 PM - 2:00 PM 
We recently used a trianionic pincer ligand to prepare group 15 triamido complexes that were characterized in the solid and solution phases. In this homologous series, the central element can adopt either a bent (VSEPR) or planar (non-VSPER) geometry. This talk will discuss the change in structural preferences descending the group, the consequence of structure on the electronic environment at the metal center, and why sometimes the structured determined by X-ray crystallography is not retained in solution! 

View Abstract 358


Katherine Marczenko

Additional Author

Saurabh Chitnis, Dalhousie University

One-Pot Synthesis of Heterometallic Copper-Manganese Complexes with Polyfunctional Imidoyl Amidine Ligands

2:00 PM - 2:20 PM 
Bidentate ligands such as acetylacetonate (acac) and 1,3-diketoiminate (nacnac), or tridentate ligands such as terpyridine (terpy), are often employed to isolate metallic complexes for a diverse range of applications including water splitting, organic catalysis, molecular magnets and photosensitizers to name a few. In that regard, the N-2-pyrimidylimidoyl-2-pyrimidylamidine (PmImAm) ligand is an excellent candidate for the development of coordination complexes as it possesses both a bidentate coordination site similar to acac and nacnac, as well as a tridentate terpy like coordination site. Having these two types of coordination environments within the same complex provides an avenue to explore polynuclear mixed metal complexes. While heterometallic complexes are typically prepared in a step-wise manner by first isolating a mononuclear complex then using it as a starting material to coordinate a second metal ion, by taking advantage of the two distinctive coordination sites in PmImAm we have achieved heterometallic copper-manganese complexes via a one-pot synthesis. Furthermore, through ppm level control over the degree of hydration (e.g., 300 ppm vs. 10000 ppm), the nuclearity and topology of these polynucelar heterometallic complexes can be tailored. This presentation will describe both a trinuclear complex with a central square planar Cu(II) ion coordinated in the bidentate pocket of PmImAm, and two peripheral penta-coordinate Mn(II) ions in the terpy-like site, as well as a hexanuclear complex with four penta-coordinate Mn(II) ions and two penta-coordinate Cu(II) ions. This presentation will focus on the synthesis and structural analysis of these complexes via single crystal X-ray diffraction, as well as their magnetometry studies. 

View Abstract 157


Raúl Castañeda, University of Ottawa Ottawa

Additional Author(s)

Mathieu Rouzières, Université du Bordeaux Pessac, FM 
Rodolphe Clérac, Université du Bordeaux Pessac, FM 
Jaclyn L. Brusso, Department of Chemistry and Biomolecular Sciences, University of Ottawa Ottawa, Ontario 

New methods to capture insoluble, unstable titanium (IV) species in single-crystal form.

2:20 PM - 2:40 PM 
The coordination of titanium (IV) halides to neutral L-type ligands and L-L type chelates results in fascinating geometries, brilliant colors unusual for a d0 species, and unusual changes in Ti-X bond lengths. In spite of being a small, hard, highly lewis-acidic metal center, Ti (IV) can surprisingly form eight-coordinate complexes with such ligands. However, TiX4(L)2 or TiX4(L-L) species are typically unstable in solution when soluble, and more often than not, intractable solids that do not dissolve in common organic solvents. A methodology has been created for small-scale TiX4-ligand reactions that result in direct formation of high-quality single crystals. The method has been utilized in elucidating the structures of several insoluble titanium complexes that have evaded crystallographic characterization for generations. 

View Abstract 308


Mrittika Roy, University of California, Davis Davis, CA 

Additional Author(s)

Marilyn Olmstead, Dept of Chemistry, Univ of California Davis
Alan Balch, University of California, Davis Davis, CA 

Towards Engineering the Polymorphs of Cocrystals

2:40 PM - 3:00 PM 
Recently we reported the ability of the anti-malarial drug 11-azaartemisinin to form cocrystals with a variety of coformers. [1-3] For carboxylic acids roughly 50% of systems studied allowed formation of cocrystals driven by a well-preserved lactam-acid synthon. In a series of arylsulfonyl derivatives of 11-azaartemisinin we further demonstrated that new polymorphs could be accessed via seeds of the molecular analogues in which the aryl group substituents were varied by single point 'atomic mutation' resulting in a different structure type. [4] We were interested to see whether a combination of these two approaches could allow extension of this route to afford polymorphs of molecular cocrystals. As a first step we have now prepared 15 substituted variations of the cocrystal between 11-azaartemisinin and salicylic acid (11-Aza:SalA) using substituted SalA compounds. In all cases to-date a molecular pair with retained synthon is present (Fig 1) and these form 2-fold screw stacks with similar geometry. In some cases (e.g. from 5-Br-SalA, 5-I-SalA) the products are clearly isostructural with the parent cocrystal, which has a monoclinic P21 polar structure with Z' =1 and just have simple lattice expansion. Others might be deemed 'homostructural' with highly related packings, but with slippage of molecular layers so that the interactions and contacts between the 1D stacks are modified. (4-Br-SalA) Further variations include doubling of asymmetric unit to create two independent stacks, that have opposite 'polarity' whilst still being P21, (5-Cl-SalA). Polarity reversal is also possible by adopting an orthorhombic P212121 arrangement, again with a 'doubled' cell. (Fig 2, 3,5-Cl-SalA). Quadrupled axis systems are also identified so that the chiral 1D stacks are rotated in either 41 or 43 screw manner. (e.g. 3-Me-SalA, 5-Me-SalA respectively) A total of seven structurally distinct ways of arranging the 1D stacks have been identified which might be deemed 'Quasi-polymorphs'. That is they each represent a possible packing of the basic 11-Aza:SalA molecular pair. We are now proceeding to see whether seeding using one form can induce another cocrystal to adopt the alternative arrangement and hence a true polymorph of the same cocrystal composition and will report our current findings. References 1. Nisar et al., Acta Cryst. (2017). A73, a268. 2. Nisar et al., CrystEngComm (2018). 20, 1205-1219. 3. Nisar et al., Acta Cryst. (2018). C74, 742-751. 4. Nisar et al., Acta Cryst. (2018). A74, a104. 

View Abstract 166


Ian WILLIAMS, HKUST Clear Water Bay

Additional Author(s)

Keyao LI, Hong Kong University of Science and Technology Clear Water Bay, Hong Kong, China 
Herman H-Y. SUNG, Hong Kong University of Science and Technology Clear Water Bay, Hong Kong, China 
Monalisa ROY, Hong Kong University of Science and Technology Clear Water Bay, Hong Kong, China 
Madiha NISAR, Hong Kong University of Science and Technology Clear Water Bay, Hong Kong, China