Recent updates to the Jmol program have added significant capabilities for crystallographic visualization and education, specifically in the area of space groups and model building. Using either the Jmol Java application or its web-based JavaScript equivalent, one can can quickly build a model given a space group and setting, generate atoms at any of the Wyckoff positions, color atoms by position or site, display all the symmetry elements within a unit cell, and generate representations of the transformations that relate any two atoms or molecules. Built-in commands allow structure retrieval from external databases including the Crystallography Open Database, American Mineralogist Crystal Structure Database, and the AFLOW Encyclopedia of Crystallographic Prototypes. Atoms can be manipulated interactively, and the positions of all symmetry-related atoms are updated with constraints for atoms on special positions. In this talk we will demonstrate some of these new features and suggest ways that both the standalone application and simple web pages can be used to engage students and help them develop a deeper understanding of crystallography.

The title compound, catena-poly[[tri-aqua-sodium]-di-μ-aqua-[tri-aqua-sodium]-μ-(ethane-1,2-di-yl)bis-[(3-meth-oxy-prop-yl)phosphinodi-thiol-ato]], [Na2(C10H22O2P2S4)(H2O)8] n , crystallizes in the triclinic space group P1. The dianionic [CH3O(CH2)3P(=S)(S-)CH2CH2P(=S)(S-)(CH2)3OCH3]2- ligand fragments are joined by a dicationic [Na2(H2O)8]2+ cluster that includes the oxygen of the meth-oxy-propyl unit of the ligand to form infinite chains.

Dithieno[3,2-b:2 ',3 '-d]thiophene (DTT) is a common molecular motif in organic electronics. We find that it forms a 1:1 charge-transfer complex (CTC) with the electron acceptor 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ). The 1:1 complex has an alternating donor/acceptor mixed-stack structure, and an intense near-infrared absorption band. Vibrational spectroscopy and electronic structure calculations are used to further understand the partial ionization induced by the DTT/DDQ complex.

In the title compound, the dianionic [CH3O(CH2)3P(=S)(S—)CH2CH2P(=S)(S—)(CH2)3OCH3]2− ligand fragments are joined by a dicationic [Na2(H2O)8]2+ cluster that includes the oxygen of the meth­oxy­propyl unit of the ligand to form infinite chains.

The title compound, catena-poly[[triaquasodium]-di-μ-aqua-[triaquasodium]-μ-(ethane-1,2-diyl)bis[(3-methoxypropyl)phosphinodithiolato]], [Na2(C10H22O2P2S4)(H2O)8] n , crystallizes in the triclinic space group P 1. The dianionic [CH3O(CH2)3P(=S)(S—)CH2CH2P(=S)(S—)(CH2)3OCH3]2− ligand fragments are joined by a dicationic [Na2(H2O)8]2+ cluster that includes the oxygen of the methoxypropyl unit of the ligand to form infinite chains.

Intermolecular interactions govern the optical and electronic properties of organic semiconductor thin films. Optimizing the function of molecular devices such as organic solar cells and light emitting diodes relies on understanding structural effects in a heterogeneous film environment. Because organic thin films are typically more disordered than inorganic crystalline semiconductors, advanced techniques are often needed to sufficiently characterize these materials. However, polarized infrared reflectance measurements are a benchtop method that can provide well-resolved vibrational spectra with specificity in their molecular orientation. By using infrared reflectance-absorbance spectroscopy (IRRAS) we relate the effects of intermolecular packing geometry on thin film vibrational spectra of perylene diimide (PDI), a prototypical molecular semiconductor. We analyze a suite of PDIs with differing sidechain substitutions, which adopt distinct crystal packing arrangements in thin films, by comparison of the reflectance spectra to isotropic KBr mixtures. We observe differences in the degree of Davydov splitting as a function of displacement along the short and long molecular axes and the π-π stacking distance that are evident in either the symmetric or anti-symmetric CO stretching frequencies of the solid. The four PDIs also display changes in relative intensity between the two modes that indicate different average molecular orientations.

Molecular doping can increase conductivity in organic semiconductor solids through the addition of an electron donor or acceptor into the organic host matrix, when ground state charge transfer interactions are induced between the matrix and the dopant that facilitate carrier transport. Aryl-substituted diketopyrrolopyrroles are common motifs in both small molecules and polymers used for organic electronics, but their molecular doping has only begun to be explored. In this work, we describe a ground state charge transfer complex between a bis(thiophene) diketopyrrolopyrrole (TDPP) as the donor and 2,3-dicyano-5,6-dichlorobenzoquinone (DDQ) as the acceptor. DDQ is a low-cost, relatively stable electron acceptor that we propose is a promising molecular dopant for TDPP-based organic materials. We report the structure of the TDPP/DDQ 1:1 co-crystal, within which we observe strong p-p interactions not only between TDPP and DDQ but also between TDPPs. In thin films prepared from a 1:1 precursor solution, we characterize the energy of the low-energy charge transfer band with UV-Vis absorption spectroscopy and observe a shift in the DDQ nitrile stretch to a lower frequency through Fourier transform infrared (FTIR) spectroscopy, confirming the presence of the ground state charge transfer complex. Single-crystal bond lengths and density functional theory are used to estimate the degree of charge transfer.

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.

The coordination polymer copper(I) 2-hydroxyethanethiolate, (CuSCH2CH2OH)n, though insoluble in all common solvents, dissolved readily in basic aqueous solutions of the thiolate anion (HOCH2CH2S-) of 2-mercaptoethanol to form a single species: the tetranuclear cluster [Cu4(mu-SCH2CH2OH)6](2)-. From this solution were grown X-ray quality single crystals of copper(I) 2-hydroxyethanethiolate. This compound underwent a hitherto unknown crystal phase transition at ca. 6 C, from point group P2(1)2(1)2(1) to Pna21, with noticeable changes in the geometry of the Cu-S layer and in the orientation of the alkylthiolate side chains. When the bulky base tetrabutylammonium hydroxide was employed in the aqueous thiolate solution used to dissolve (CuSCH2CH2OH)n, the water-soluble polynuclear copper(I) complex bis(tetrabutylammonium) hexakis(mu-2-hydroxyethanethiolato) tetracuprate(I), [(C4H9)4N](2)[Cu4(mu-SCH2CH2OH)(6)], could be isolated as X-ray quality crystals. Structural characterization of this complex revealed a tetrahedral arrangement of copper(I) centers with thiolates bridging the edges of the tetrahedra. On standing, this complex degraded to a larger polynuclear Cu(I) sulfide cluster.

We have developed a website that illustrates fundamental unit-cell types, unit cell contents, close packing of atomic layers, and the structures of selected elements and ionic materials.A companion set of 3D-printed models of the unit cell contents of simple cubic, body-centered cubic, face-centered cubic, and hexagonal close-packed structures helps students connect the computer representations to physical models.We have incorporated these materials into our first-year chemistry laboratory course, enhancing a model-building exercise with computer representations and 3D building blocks to demonstrate lattice-point sharing, packing efficiency, and coordination number.Additional web-based materials for teaching symmetry have been extended to include crystallographic point groups and the symmetry-relationships found in selected space groups and are suitable for use in upper-level undergraduate courses.While students may have been introduced to symmetry in other courses such as Inorganic or Physical Chemistry, these resources emphasize crystallographic symmetry and the notation used within crystallography.Additionally, we have developed an interactive 2D Fourier transform website that demonstrates the reciprocal relationships found in diffraction.This site serves as a natural extension to the popular optical transform demonstration.

Ionic co-crystals are co-crystals between organic mol-ecules and inorganic salt coformers. Co-crystals of pharmaceuticals are of inter-est to help control polymorph formation and potentially improve stability and other physical properties. We describe the preparation, crystal structures, and hydrogen bonding of five different 2:1 benzamide or tolu-amide/zinc(II) chloride co-crystal salts, namely, bis-(benzamide-κO)di-chlorido-zinc(II), [ZnCl2(C7H7NO)2], di-chlor-ido-bis-(2-methyl-benzamide-κO)zinc(II), [ZnCl2(C8H9NO)2], di-chlorido-bis-(3-methyl-benzamide-κO)zinc(II), [ZnCl2(C8H9NO)2], di-chlorido-bis-(4-methyl-benzamide-κO)zinc(II), [ZnCl2(C8H9NO)2], and di-chlorido-bis-(4-hy-droxy-benzamide-κO)zinc(II), [ZnCl2(C7H7NO2)2]. All of the complexes contain hydrogen bonds between the amide N-H group and the amide carbonyl oxygen atoms or the chlorine atoms, forming extended networks.

The crystal structures of two polymorphic forms of 1-butyl-3-methylimidazolium nitrate are reported. The form observed at 100 K and 200 K (Ia and Ib) crystallizes in the $$P{\bar{1}}$$ space group and contains two independent imidazolium cations and nitrate anions. At 100 K the butyl chain of one cation adopts a TT (trans–trans) conformation and the other cation adopts a G′G′ (gauche–gauche) conformation. At 200 K, the G′G′ chain is disordered with about twelve percent of the GT conformation present. A different polymorph (Form II, also crystallizing in the $$P{\bar{1}}$$ space group with two independent ion pairs) is present at 273 K displaying significant disorder in the butyl chains with a mixture of G′T, G′G′, and GT conformers. Raman spectra were collected on samples between 100 and 350 K and show changes in band frequencies and intensities consistent with conversion between different butyl chain conformations. Hydrogen bond interactions are present between cation C–H’s and oxygen atoms of the nitrate ions, with significant lengthening observed for three of the six close contacts (and formation of one new contact) upon conversion to the higher-temperature form. The structural details revealed in this study shed light on the intermolecular forces and the conformational changes that accompany phase changes in 1-butyl-3-methylimidazolium nitrate. X-ray diffraction and Raman spectroscopy of the ionic liquid 1-butyl-3-methylimidazolium nitrate at temperatures from 100 to 300 K showevidence of two different polymorphs and significant temperature-dependentconformational changes.

The title compound, [Mo(C 5 H 7 O 2 ) 2 O 2 ] or cis -[MoO 2 (acac) 2 ] (acac is acetylacetonate), contains a molybdenum(VI) atom coordinated by two acetylacetonate ligands and two doubly bonded oxido ligands in a distorted octahedral shape. The molecule is chiral and the asymmetric unit contains two independent molecules (one Δ, one Λ). Extensive C—H...O contacts are present throughout the structure. Data were collected at 100 K, providing higher precision of unit-cell parameters and atomic positions than previous determinations [Kamenar et al. (1973). Cryst. Struct. Commun. 2 , 41–44.; Krasochka et al. (1975). Zh. Strukt. Khim. 16 , 696–698].

While cheminformatics skills necessary for dealing with an ever-increasing amount of chemical information are considered important for students pursuing STEM careers in the age of big data, many schools do not offer a cheminformatics course or alternative training opportunities. This paper presents the Cheminformatics Online Chemistry Course (OLCC), which is organized and run by the Committee on Computers in Chemical Education (CCCE) of the American Chemical Society (ACS)’s Division of Chemical Education (CHED). The Cheminformatics OLCC is a highly collaborative teaching project involving instructors at multiple schools who teamed up with external chemical information experts recruited across sectors, including government and industry. From 2015 to 2019, three Cheminformatics OLCCs were offered. In each program, the instructors at participating schools would meet face-to-face with the students of a class, while external content experts engaged through online discussions across campuses with both the instructors and students. All the material created in the course has been made available at the open education repositories of LibreTexts and CCCE Web sites for other institutions to adapt to their future needs.

Charge-assisted hydrogen bonding plays a significant role in the crystal structures of solvates of ionic compounds, especially when the cation or cations are primary ammonium salts. We report the crystal structures of four ammonium salts of molybdenum halide cluster solvates where we observe significant hydrogen bonding between the solvent molecules and cations. The crystal structures of bis(anilinium) octa-μ3-chlorido-hexachlorido-octahedro-hexamolybdate N,N-dimethylformamide tetrasolvate, (C6H8N)2[Mo6Cl8Cl6]·4C3H7NO, (I), p-phenylenediammonium octa-μ3-chlorido-hexachlorido-octahedro-hexamolybdate N,N-dimethylformamide hexasolvate, (C6H10N2)[Mo6Cl8Cl6]·6C3H7NO, (II), N,N′-(1,4-phenylene)bis(propan-2-iminium) octa-μ3-chlorido-hexachlorido-octahedro-hexamolybdate acetone trisolvate, (C12H18N2)[Mo6Cl8Cl6]·3C3H6O, (III), and 1,1′-dimethyl-4,4′-bipyridinium octa-μ3-chlorido-hexachlorido-octahedro-hexamolybdate N,N-dimethylformamide tetrasolvate, (C12H14N2)[Mo6Cl8Cl6]·4C3H7NO, (IV), are reported and described. In (I), the anilinium cations and N,N-dimethylformamide (DMF) solvent molecules form a cyclic R42(8) hydrogen-bonded motif centered on a crystallographic inversion center with an additional DMF molecule forming a D(2) interaction. The p-phenylenediammonium cation in (II) forms three D(2) interactions between the three N—H bonds and three independent N,N-dimethylformamide molecules. The dication in (III) is a protonated Schiff base solvated by acetone molecules. Compound (IV) contains a methyl viologen dication with N,N-dimethylformamide molecules forming close contacts with both aromatic and methyl H atoms.

The Advanced Laboratory course at Otterbein University is a required course combining a set of fourweek research rotations with integrated scientific writing and presentation activities.The challenge from a faculty member's perspective is designing a time-limited research experience involving students with a wide range of prior coursework.I will describe how our students explored the preparation of ionic cocrystals of a variety of drug or drug-like molecules that they then subsequently characterized by powder and single-crystal X-ray diffraction, DSC, TGA and FTIR.Six new crystal structures (along with several redeterminations) were completed in the course of the one semester course.While not a crystallography course, the research experience required that students become familiar with crystal-growing techniques, solventassisted mechanochemistry, unit cell determination, basic X-ray sample handling and processing and structural database searching.The experiments were well-suited to the limited time scale of the course, engaging to students of diverse interests and experimentally accessible.