Cool Structures

Conference: 2021: 71st ACA Annual Meeting
08/03/2021: 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.


Understanding Intermetallic Intergrowths and Reactivity: Chemical Pressure-Driven Epitaxy Between Domain Interfaces

The immense structural diversity of intermetallic phases offers promising avenues for accessing a wide range of materials with desirable properties. Although the development of design principles to guide the targeted synthesis of such materials is still needed, common themes arising in this class of materials show that even the most complicated structures can be understood in terms of intergrowth domains. Specifically, previous works have shown that the Ca3Cu7.8Al26.2 phase can be interpreted as a Chemical Pressure (CP) driven intergrowth between CaAl4 and CuAl2 units, which is further stabilized by electronegativity anchors. More recently, we have seen similar atomic packing considerations extended to a series of Frank-Kasper phases in the Mo-Fe-Cr system. Continuing this theme, we will present a new example in the Y-Ni system where the major packing issues present in the CaCu5-type parent structure serve as the major driving force for its intergrowth with YNi2 laves layers, with opportunities for stabilizing epitaxial interactions arising at the domain interfaces. It is through these examples that we aspire to illustrate a lens through which we can inform the design of new modular materials with multifunctional properties. 

View Abstract 720


Kyana Sanders, University of Wisconsin, Madison Madison, WI 

Additional Author

Daniel Fredrickson, University of Wisconsin, Madison Madison, WI 

Fully fluorinated Pd(F6acac) complexes: polymorphism and fluorine-fluorine interactions.

Weak intermolecular interactions such as hydrogen bond, π-π stacking, and halogen bond, play a crucial role in stabilizing crystal packing and in the formation of polymorphs and supramolecular motifs. Among the weak intermolecular interactions, fluorine-fluorine and hydrogen-fluorine interactions are expected to provide only a small stabilization contribution to the crystal packing and they are often considered non-stabilizing. [1, 2] For this reason, their role in influencing the solid state properties of a compound is still questioned. F···F short contacts, with F···F distance shorter than the sum of the VdW radii (2.94 Å), are usually considered a consequence of tight crystal packing. However, there are examples of fluorinated compounds where F···F interactions are the driving force of the crystal packing, or at least they provide energy stabilization, contributing to the formation of patterns, motifs, and polymorphs. [3, 4]

We present a study on the polymorphism of a fully fluorinated Pd dimer prepared by reaction of palladium bis(hexafluoroacetylacetonate) (Pd(F6acac)2) with pentafluoroaniline (PFA). PFA is deprotonated upon coordination with two palladium atoms, forming a N-bridged dimer (Fig 1.). The PFA ligands in the dimer can either have trans or cis conformation. Due to the presence of 22 fluorine atoms in the dimer, different F-F interactions are possible in the packing, generating polymorphs for both the trans and the cis stereoisomer. In addition to the polymorphs, we also characterized several solvate co-crystals. All the crystal structures observed have multiple F···F short contacts (2.647 - 2.934 Å). The crystals of the trans complex also undergo a reversible structural transformation from triclinic (P -1) to monoclinic (P 21/c) in the temperature range 220-221 K. The transformation is noticeable as systematic absences corresponding to the 21 screw axes appear at T > 221 K in the diffraction pattern (Fig. 2).

[1] Berger, R., Resnati, G., Metrangolo, P., Weber, E.; Hulliger (2011), J. Chem. Soc. Rev., 40, 3496.
[2] Panini, P. & Chopra, D. (2015) Hydrogen Bonded Supramolecular Structures, edited by Z. Li and L. Wu, vol. 87, Springer.
[3] Bayón, R., Coco, S., Espinet, P., (2005) Chem. Eur. J., 11, 1079.
[4] Mariaca, R., Behrnd, N.-R., Eggli, P., Stoeckli-Evans, H., Hulliger, J., (2006), CrystEngComm, 8, 222. 

View Abstract 592


Veronica Carta, Indiana University Bloomington, IN 

Additional Author(s)

Aniffa Kouton, Indiana University Bloomington, IN 
Allen Siedle, Indiana University Bloomington, IN 

Small Molecule Microcrystal Electron Diffraction (MicroED) for the Pharmaceutical Industry – Lessons Learned from Examining Over Fifty Samples

The emerging field of microcrystal electron diffraction (MicroED) is of great interest to industrial researchers working in the drug discovery and drug development space. The promise of being able to routinely solve high-resolution crystal structures without the need to grow large crystals is very appealing. Despite MicroED's exciting potential, adoption across the pharmaceutical industry has been slow, primarily owing to a lack of access to specialized equipment and expertise. Here we will present our experience building a small molecule MicroED service pipeline for members of the pharmaceutical industry. In the past year, we have examined more than fifty small molecule samples submitted by our clients, the majority of which have yielded data suitable for structure solution. We will also detail our experience determining small molecule MicroED structures of pharmaceutical interest and offer some insights into the typical experimental outcomes. This experience has led us to conclude that small molecule MicroED adoption will continue to grow within the pharmaceutical industry where it is able to rapidly provide structures inaccessible by other methods. 

View Abstract 701


Jessica Bruhn, NanoImaging Services Oceanside, CA 

Additional Author(s)

Giovanna Scapin, NanoImaging Services San Diego, CA 
Anchi Cheng, NanoImaging Services San Diego, CA 
Brandon Mercado, Yale University New Haven, CT 
David Waterman, STFC Didcot
Thejusvi Ganesh, NanoImaging Services San Diego, CA 
Sargis Dallakyan, NanoImaging Services San Diego, CA 
Brandon Read, NanoImaging Services San Diego, CA 
Travis Nieusma, NanoImaging Services San Diego, CA 
Kyle Lucier, NanoImaging Services San Diego, CA 
Megan Mayer, Harvard Medical School Boston, MA 
Nicole Chiang, NanoImaging Services San Diego, CA 
Nicole Poweleit, NanoImaging San Diego, CA 
Philip McGilvray, NanoImaging Services San Diego, CA 
Clint Potter, NanoImaging Services San Diego, CA 
Bridget Carragher, NanoImaging Services San Diego, CA 

Coffee Break

The First X-ray Crystal Structures of 5,5,10,10-Tetrahalotricyclo[,6]decanes

While a number of bicyclo and tricyclo compounds have been extensively studied (the norbornanes come to mind), other tricyclic compounds remain relatively uncharacterized. To this end, tetrahalogenated tricyclo[,6]decanes have been synthesized to be characterized by x-ray crystallographic methods. Halogenation raises the melting point and provides for a convenient synthetic method of cyclopropanation of 1,5-cyclooctadiene to produce crystals suitable for x-ray diffraction. Our laboratory has now synthesized six bromine and chlorine substituted tricyclo[,6]decanes and we are currently analyzing these compounds structurally.

While one of these compounds was synthesized by Louis Fieser and the space group determined by Jean Hartsuck and William N. Lipscomb in the 1960s, a high resolution structure was never produced. Among the challenges of solving these structures is that the tricyclodecane rings have at times exhibited significant ring disorder, and perhaps this accounts for the lack of a structure from the Harvard investigation of years ago. The cyclooctane rings are highly puckered, providing a number of opportunities for disordered arrangement of the fairly flexible rings. Of these compounds, 5,5,10,10-tetrabromotricyclo[]decane, while puckered, was not disordered. 5,5,10,10-tetrachlorotricyclo[]decane, on the other hand, exhibited at least two puckered structures superimposed on one another. The average structure resembles a boat form cyclohexane, consistent with Hartsuck and Lipscomb's original work.

To our knowledge, these structures represent the first x-ray crystal structures of any tricyclo[]decanes. 

View Abstract 687


Kent Clinger

Additional Author(s)

Eric Reinheimer, Rigaku Americas Corporation The Woodlands, TX 
James R. Boone, Lipscomb University Nashville, TN 
Robert L. King, Lipscomb University Nashville, TN 

The Many Moods of the 3-Aminopyridinium Chlorocuprate(II) System

Our group has previously reported the structure of bis(3-aminopyridinium) tetrachlorocuprate(II) (as a possible correction to the published structure, CSD refcode: PATMUT). This compound was serendipitously obtained as red crystals from acetonitrile using a thermal gradient technique on a green solid that in turn was obtained by evaporation of a 6 M HCl solution of 3-aminopyridine and CuCl2.2H2O in a 2:1 molar ratio. We have since made a more systematic study, first by thermal gradient crystal growth with green crystals of 3-ammoniumpyridinium tetrachlorocuprate(II) (SAGJIT, grown by the method of Willett et al., JACS (1988), 110, 8639) as the source material in a variety of organic solvents. Growth in acetonitrile yielded crystals of SAGJIT. However, growth in 1-proponal yielded green crystals of a new compound, bis(3-aminopyridinium)dichlorodi-μ-chlorodicuprate(II), consisting of an asymmetrically bridged dimer. This is in contrast to red crystals of the symmetrically bridged analog (GAGNOR) reported by Blanchette and Willett (Inorg. Chem. (1988), 27, 843), but similar to their reported asymmetrically bridged bromide dimer (GAGNUX). Crystal growth in methylethylketone yields an extremely dark solution and a dark solid mass containing lighter crystals of 3-ammoniumpyridinium chloride and a darker, as yet undetermined solid, while crystal growth in tetrahydrofuran has proceeded very slowly. The green source crystals of SAGJIT were then also ground together with a stoichiometric amount of 3-aminopyridine. This yielded a red solid which was loaded into thermal gradient tubes. Growth in acetonitrile yielded red crystals of the desired bis(3-aminopyridinium) tetrachlorocuprate(II), consisting of isolated CuCl42- flattened tetrahedral. Growth in 1-proponal yielded orange crystals of the same stoichiometry, but formulated as 3-aminopyridinium (3-aminopyridinium)tetrachlorocuprate(II). This new compound contains isolated 5-coordinate complexes, each containing a coordinated 3-aminopyridinium cation, which are separated by 3-aminopyridinum counterions The complex assumes a geometry intermediate between tbp and sp, with the 3-aminopyridinium cation axial and basal, respectively, and forming a trans N-Cu-Cl angle of 178°. The three basal chlorides have a Cu-Cl bond lengths of ~2.3 Å, with a trans Cl-Cu-Cl angle of 154°, and an apical Cu-Cl bond length of 2.54 Å. 

View Abstract 569


Marcus Bond, Dept of Chemistry and Physics, Southeast Missouri State University Cape Girardeau, MO 

Additional Author

Adeeta Balkaransingh, Southeast Missouri State University Cape Girardeau, MO 

Variable Temperature Polymorphism of 2-benzoyl-N,N-diethylbenzamide

2-Benzoyl-N,N-diethylbenzamide (BDB) was first synthesized as a potential candidate for antispasmodic drugs by Sakamoto et al. (1950) and the thermal profile of the compound was studied by the author (m.p. = 51.1 °C) [1]. The compound was also studied by different research groups where a different value of melting point was reported (m.p. = 76 -77 °C) [2,3]. It is known that different polymorphs can have different physicochemical properties however, the crystal structures of BDB were not elucidated, and assign the correct form of BDB with the melting point was not possible. In 2004 the compound was synthesized by Sakamoto et al. as a precursor for asymmetric synthesis and the crystal structure of an orthorhombic form of BDB was obtained. However, the melting point of this form was not reported by the author [4]. This work aims to assign the melting point with the correct polymorph of BDB and screen for new polymorphs in non-ambient conditions. Here, we identify new phases of BDB using single-crystal x-ray diffraction and variable temperature x-ray powder diffraction and establish the correlation between crystal structure and thermal properties for this compound.

[1] M. Protiva, Z. J. Vejdělek. Collect. Czech. Chem. Commun. 1950, 15, 541-551.
[2] W. M. Seganish, P. DeShong, Journal of Organic Chemistry. 2004, V69(20), P6790-6795.
[3] J. W. Lynn, J. English Jr, Journal of Organic Chemistry. 1951, V16, P1546-55.
[4] M. Sakamoto, S. Kobaru, T. Mino, T. Fujita; Chemical Communications. 2004, (8), P1002-1003. 

View Abstract 503


Lygia Silva de Moraes, Université Libre de Bruxelles Rio de Janeiro

Additional Author(s)

Jie Liu, Université Libre de Bruxelles Bruxelles
Elumalai Gopi, Université Libre de Bruxelles Bruxelles
Ryusei Oketani, Université Libre de Bruxelles Bruxelles
Alan Robert Kennedy, University of Strathclyde Glasgow
Yves Henri Geerts, Université Libre de Bruxelles Bruxelles

Water Soluble Picolamidine Metal Complexes

Water-soluble complexes are attractive in many fields including but not limited to water splitting, polymer catalysis, and MRI contrast agents. In this work picolinamidine (PiAm; Chart 1) was used to build six different water-soluble complexes (1-6; Chart 1) with copper, nickel and zinc and they were studied by X-ray single crystal diffraction, IR, UV-vis, and PXRD. Amidine ligands in general had not extensively been used in coordination chemistry, and PiAm has a great potential to build water-soluble complexes as the amidine group is capable to act both as hydrogen bond donor and acceptor. By design it is possible to control the number of ligands coordinated to individual metal ions, for example 1 and 2 (Chart 1) have only one ligand coordinated while 3-6 (Chart 1) have two PiAm ligands coordinated to the metal ions. Complexes 1 and 2 are very similar with the main difference being the substitution of one chlorine atom for one bromine atom. Unsurprisingly these complexes are isomorphic with the monoclinic P21/n space group and a minor increase of 4.5% of the total unit cell volume for 2 due to the change of chlorine for bromine. Complexes 3, 4, and 5 share a similar framework with the metal ion located at an inversion center, resulting in the same ligands opposite to each other, in an octahedral cis configuration. Despite the similarities between 3 and 4, only one single crystalline phase was found for 3, whereas two different polymorphic structures were found in the case of 4 (4a and 4b). Both 4a and 4b have the monoclinicP21/n space group and 4a is isomorphic to 3. The differences in coordination of these complexes along the differences in hydrogen bonding and crystal packing will be discussed in this work. In conclusion, PiAm was successfully used to synthesize six different complexes with remarkable water solubility and stability and further studies will be underway for the copper complexes to measure their activity as MRI contrast agents. 

View Abstract 508


Raúl Castañeda, New Mexico Highlands University las vegas, NM 

Additional Author(s)

Michael Petronis, New Mexico Highlands University Las Vegas, NM 
Tatiana Timofeeva, Chemistry Dept, New Mexico Highlands Univ