Janine George

Intermolecular contacts in bromomalonic aldehyde—intuition, experiment, and theory

Mutually perpendicular hydrogen bonds, halogen bonds and stacking interactions are investigated in the seemingly simple crystal structure of bromomalonic aldehyde (C3H3O2Br). This combined experimental and theoretical study sheds new light on the role of electrostatic interactions in molecular crystalline networks and poses a caveat to look beyond what may be termed “chemical intuition”.

β-CuN3: the overlooked ground-state polymorph of copper azide with heterographene-like layers.

An unexpected polymorph of the highly energetic phase CuN3 has been synthesized and crystallizes in the orthorhombic space group Cmcm with a=3.3635(7), b=10.669(2), c=5.5547(11) Å and V=199.34(7) Å(3). The layered structure resembles graphite with an interlayer distance of 2.777(1) Å (=1/2 c). Within a single layer, considering N3(-) as one structural unit, there are 10-membered almost hexagonal rings with a heterographene-like motif. Copper and nitrogen atoms are covalently bonded with Cu-N bonds lengths of 1.91 and 2.00 Å, and the N3(-) group is linear but with N-N 1.14 and 1.20 Å. Electronic-structure calculations and experimental thermochemistry show that the new polymorph termed β-CuN3 is more stable than the established α-CuN3 phase. Also, β-CuN3 is dynamically, and thus thermochemically, metastable according to the calculated phonon density of states. In addition, β-CuN3 exhibits negative thermal expansion within the graphene-like layer.

Anisotropic displacement parameters from dispersion-corrected DFT methods and their experimental validation by temperature-dependent X-ray diffraction

In chemical crystallography, the thermal motion of scattering centres is commonly described by anisotropic displacement parameters (ADPs). Very recently, it has been shown that ADPs are not only accessible by diffraction experiments but also via theory: this emerging approach seems promising but must be thoroughly tested. In this study, we have performed specifically tailored X-ray diffraction (XRD) experiments in fine steps between 100 and 300 K which allow detailed comparison to ab initio data from dispersion-corrected density functional theory (DFT) combined with periodic lattice-dynamics. The compound chosen for this study, crystalline pentachloropyridine (C5NCl5), is well suited for this purpose: it represents a molecular crystal without H atoms, thus posing no challenge to XRD; its solid-state structure is controlled by dispersion and halogen-bonding interactions; and the ADPs associated with the peripheral Cl atoms show strong temperature dependence. Quality criteria in direct and in reciprocal space prove that ADPs are predicted with high confidence for the temperature range between 100 and 200 K, and that several economic dispersion corrections to DFT can be reliably employed for this purpose. Within the limits we have explored here, the ab initio prediction of ADPs appears to be a facile and complementary tool, especially in those cases where diffraction data cannot provide a straightforward model for thermal motion.

Tetrel Bonds in Infinite Molecular Chains by Electronic Structure Theory and Their Role for Crystal Stabilization

Intermolecular bonds play a crucial role in the rational design of crystal structures, dubbed crystal engineering. The relatively new term tetrel bonds (TBs) describes a long-known type of such interactions presently in the focus of quantum chemical cluster calculations. Here, we energetically explore the strengths and cooperativity of these interactions in infinite chains, a possible arrangement of such tetrel bonds in extended crystals, by periodic density functional theory. In the chains, the TBs are amplified due to cooperativity by up to 60%. Moreover, we computationally take apart crystals stabilized by infinite tetrel-bonded chains and assess the importance of the TBs for the crystal stabilization. Tetrel bonds can amount to 70% of the overall interaction energy within some crystals, and they can also be energetically decisive for the taken crystal structure; their individual strengths also compete with the collective packing within the crystal structures.

Lattice thermal expansion and anisotropic displacements in -sulfur from diffraction experiments and first-principles theory

Thermal properties of solid-state materials are a fundamental topic of study with important practical implications. For example, anisotropic displacement parameters (ADPs) are routinely used in physics, chemistry, and crystallography to quantify the thermal motion of atoms in crystals. ADPs are commonly derived from diffraction experiments, but recent developments have also enabled their first-principles prediction using periodic density-functional theory (DFT). Here, we combine experiments and dispersion-corrected DFT to quantify lattice thermal expansion and ADPs in crystalline α-sulfur (S8), a prototypical elemental solid that is controlled by the interplay of covalent and van der Waals interactions. We begin by reporting on single-crystal and powder X-ray diffraction measurements that provide new and improved reference data from 10 K up to room temperature. We then use several popular dispersion-corrected DFT methods to predict vibrational and thermal properties of α-sulfur, including the anisotropic lattice thermal expansion. Hereafter, ADPs are derived in the commonly used harmonic approximation (in the computed zero-Kelvin structure) and also in the quasi-harmonic approximation (QHA) which takes the predicted lattice thermal expansion into account. At the PPBE+D3(BJ) level, the QHA leads to excellent agreement with experiments. Finally, more general implications of this study for theory and experiment are discussed.

On the DFT ground state of crystalline bromine and iodine.

We report on an erroneous ground state within common density functional theory (DFT) methods for the solid elements bromine and iodine. Phonon computations at the GGA level for both molecular crystals yield imaginary vibrational modes, erroneously indicating dynamic instability-that fact alone could easily pass as a computational artefact, but these imaginary modes lead to energetically more favorable and dynamically stable structures, made up of infinite monoatomic chains. In contrast, meta-GGA and hybrid functionals yield the correct energetic order for bromine, while for iodine, most global hybrids do not improve the GGA result significantly. The qualitatively correct answer, in both cases, is given by the long-range corrected hybrid LC-ωPBE, the Minnesota functionals M06L and M06, and by periodic Hartree-Fock and MP2 theory. This poor performance of economic DFT functionals should be kept in mind, for example, during global structure optimizations of systems with significant contributions from halogen bonds.

Ammonothermal Synthesis, Crystal Structure, and Properties of the Ytterbium(II) and Ytterbium(III) Amides and the First Two Rare-Earth-Metal Guanidinates, YbC(NH)3 and Yb(CN3H4)3

We report the oxidation-controlled synthesis of the ytterbium amides Yb(NH2)2 and Yb(NH2)3 and the first rare-earth-metal guanidinates YbC(NH)3 and Yb(CN3H4)3 from liquid ammonia. For Yb(NH2)2, we present experimental atomic displacement parameters from powder X-ray diffraction (PXRD) and density functional theory (DFT)-derived hydrogen positions for the first time. For Yb(NH2)3, the indexing proposal based on PXRD arrives at R3̅, a = 6.2477(2) Å, c = 17.132(1) Å, V = 579.15(4) Å(3), and Z = 6. The oxidation-controlled synthesis was also applied to make the first rare-earth guanidinates, namely, the doubly deprotonated YbC(NH)3 and the singly deprotonated Yb(CN3H4)3. YbC(NH)3 is isostructural with SrC(NH)3, as derived from PXRD (P63/m, a = 5.2596(2) Å, c = 6.6704(2) Å, V = 159.81(1) Å(3), and Z = 2). Yb(CN3H4)3 crystallizes in a structure derived from the [ReO3] type, as studied by powder neutron diffraction (Pn3̅, a = 13.5307(3) Å, V = 2477.22(8) Å(3), and Z = 8 at 10 K). Electrostatic and hydrogen-bonding interactions cooperate to stabilize the structure with wide and empty channels. The IR spectra of the guanidinates are compared with DFT-calculated phonon spectra to identify the vibrational modes. SQUID magnetometry shows that Yb(CN3H4)3 is a paramagnet with isolated Yb(3+) (4f(13)) ions. A CONDON 2.0 fit was used to extract all relevant parameters.

Synthesis, Structure, and Properties of SrC(NH)3, a Nitrogen‐Based Carbonate Analogue with the Trinacria Motif

Strontium guanidinate, SrC(NH)3 , the first compound with a doubly deprotonated guanidine unit, was synthesized from strontium and guanidine in liquid ammonia and characterized by X-ray and neutron diffraction, IR spectroscopy, and density-functional theory including harmonic phonon calculations. The compound crystallizes in the hexagonal space group P63 /m, constitutes the nitrogen analogue of strontium carbonate, SrCO3 , and its structure follows a layered motif between Sr(2+) ions and complex anions of the type C(NH)3 (2-) ; the anions adopt the peculiar trinacria shape. A comparison of theoretical phonons with experimental IR bands as well as quantum-chemical bonding analyses yield a first insight into bonding and packing of the formerly unknown anion in the crystal.

Lattice thermal expansion and anisotropic displacements in urea, bromomalonic aldehyde, pentachloropyridine, and naphthalene

Anisotropic displacement parameters (ADPs) are commonly used in crystallography, chemistry, and related fields to describe and quantify thermal motion of atoms. Within the very recent years, these ADPs have become predictable by lattice dynamics in combination with first-principles theory. Here, we study four very different molecular crystals, namely, urea, bromomalonic aldehyde, pentachloropyridine, and naphthalene, by first-principles theory to assess the quality of ADPs calculated in the quasi-harmonic approximation. In addition, we predict both the thermal expansion and thermal motion within the quasi-harmonic approximation and compare the predictions with the experimental data. Very reliable ADPs are calculated within the quasi-harmonic approximation for all four cases up to at least 200 K, and they turn out to be in better agreement with the experiment than those calculated within the harmonic approximation. In one particular case, ADPs can even reliably be predicted up to room temperature. Our results also hint at the importance of normal-mode anharmonicity in the calculation of ADPs.