The crystal structure and molecular thermal motion of urea at 12, 60 and 123 K from neutron diffraction

Swaminathan, S.; Craven, B. M.; McMullan, R. K.

doi:10.1107/s0108768184002135

Cited by 295 publications

(225 citation statements)

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“…[36][37][38] In this Communication, we present a fully-integrated ab initio quantum-mechanical theoretical framework for the study of the thermal properties of molecular crystals, which is based on: (i) the use of generalized-gradient and global hybrid functionals, a posteriori dispersion-corrected according to Grimme's D3 proposal; 39,40 (ii) the efficient use of both harmonic and quasi-harmonic lattice dynamical calculations for the description of phonon dispersion; [41][42][43][44][45] (iii) periodic boundary condition calculations making use of an atom-centered Gaussian-type function basis set of triplex quality plus polarization functions; 46,47 (iv) the use of efficient fully-automated algorithms for the calculation of the fourth-rank elastic tensor of crystals belonging to any space group of symmetry; 48 (v) the combined use of the quasi-harmonic and quasi-static approximations to include thermal effects on elastic constants; 49,50 (vi) full exploitation of both point-symmetry and efficient parallelization of all algorithms at all steps of the calculations. 51,52 The molecular crystal of urea, belonging to the tetragonal P% 42 1 m space group, is taken as a suitable test-case for a couple of reasons: (i) its thermal features (anisotropic thermal lattice expansion, [53][54][55][56][57] single-crystal elastic constants at room temperature, [58][59][60] thermodynamic properties 61,62 ) have been measured in different, independent experimental studies, thus making it the optimal system for benchmarking our computational strategy; (ii) a balanced description of most kinds of chemical interactions is required to properly describe it; furthermore, its peculiar molecular chain-like structure (see panel C of Fig. 1) leads to a high directionality of the various interactions (from intra-chain electrostatic and hydrogen-bonds to inter-chain dispersive, etc.…”

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“…1, we report the volumetric and directional (i.e. anisotropic) thermal lattice expansion of urea, as measured experimentally (more details in the ESI †) [53][54][55][56][57] and as determined by present quasi-harmonic ab initio calculations (phonons of the primitive cell evaluated at 7 distinct volumes within QHA), by minimizing F with respect to the volume at each temperature. Several DFT functionals are considered: some non-dispersion-corrected and a bunch of -D3 corrected ones.…”

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Thermal properties of molecular crystals through dispersion-corrected quasi-harmonic ab initio calculations: the case of urea

2016

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An ab initio quantum-mechanical theoretical framework is presented to compute the thermal properties of molecular crystals. The present strategy combines dispersion-corrected density-functional-theory (DFT-D), harmonic phonon dispersion, quasi-harmonic approximation to the lattice dynamics for thermal expansion and thermodynamic functions, and quasi-static approximation for anisotropic thermoelasticity. The proposed scheme is shown to reliably describe thermal properties of the urea molecular crystal by a thorough comparison with experimental data.Molecular crystals have increasingly attracted great attention due to their peculiar chemical and physical properties, which make them suitable as high energy-density materials, 1-3 active pharmaceutical ingredients (APIs), 4-6 constituents of opto-electronic devices for their linear and non-linear optical properties, 7-9 etc.Nonetheless, from a theoretical view-point, they still represent a major challenge to the state-of-the-art quantum-chemical methods as many kinds of chemical interactions (covalent intra-molecular, electrostatic, hydrogen-bond, long-range dispersive) need to be accurately described simultaneously. Only in recent years, have different theoretical approaches been devised in order to predict their structural and energetic properties (with the main goal of discriminating between competing polymorphs): from force-field to high-level molecular fragment-based schemes, from periodic dispersion-corrected density functional theory (DFT-D) to periodic many-body wave-function techniques. [10][11][12][13][14][15][16][17][18] However, once a reliable and balanced description of the various chemical interactions has been achieved by means of any of the above-mentioned quantum-chemical methods, the extension of their applicability to more complex properties of technological and industrial relevance, which would greatly increase their predictiveness, such as mechanical, elastic, optical and thermodynamic responses, [19][20][21][22] has to be performed. Apart from the intrinsic high degree of complexity of the required theoretical techniques and algorithms, the main difficulty here is represented by the fact that most of those properties are largely affected by thermal effects, 23-25 even at room temperature, such as zero-point energy, harmonic and anharmonic thermal nuclear motion, thermal lattice expansion, etc.Most quantum-chemical ab initio methods describe the groundstate of a system at zero pressure and temperature. If the inclusion of pressure in the computed structural and elastic properties is a relatively easy task, 16,[26][27][28] this is definitely not the case when temperature has to be accurately accounted for. Indeed, we are still far from having effective schemes formally developed and efficiently implemented in a solid state context, particularly so when anharmonic terms to the lattice potential have to be included into the formalism. When the harmonic approximation (HA) to the lattice potential is used, the vibrational contribution to the free ene...

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Thermal properties of molecular crystals through dispersion-corrected quasi-harmonic ab initio calculations: the case of urea

2016

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“…l.ti, #,j, Oij, V E,, Stewart & Jensen (1967) Kvick & Popelier (1992); (e) Jeffrey, Ruble, McMullan & Pople (1987); (f) Coppens (1967); (g) Jeffrey, Ruble, McMullan, DeFrees, Binkley & Pople (1980); (h) Savariault & Lehmann (1980); (i) Swaminathan, Craven & McMullan (1984); (j) Boese, Maulitz & Stellberg (1994); (k) Nijveldt & Vos (1988); (/) Kampermann, Ruble & Craven (1994).…”

Section: Compute Molecular Propertiesmentioning

confidence: 99%

Molecular electric moments and electric field gradients from X-ray diffraction data: model studies

Spackman¹,

Byrom²

1996

Acta Crystallogr Sect B

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Model X-ray data sets, with and without the inclusion of experimental thermal motion parameters, have been computed via Fourier transformation of ab initio molecular electron densities for 12 different molecular crystals. These datasets were then analysed with three different multipole models of varying sophistication and, from the multipole functions, molecular dipole and second moments, as well as electric field gradients (EFG's), at each nuclear site were computed and compared with results obtained from the original ab initio wavefunctions. The results provide valuable insight into the reliability of these properties, extracted in the same way from experimental X-ray data. Not all molecular systems display identical trends, but a general pattern is discernible. Specifically, dipole moments are typically underestimated by a small but significant amount (~ 10-15%), the trace of the second moment tensor is well determined but overestimated by a few per cent and electric field gradients at protons are confirmed to be well within reach of a careful charge density analysis of X-ray diffraction data.

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“…In the tetragonal α-form of urea, the equivalent torsion angles are 0°, as one would expect from a planar molecule. 32 In the HEX UIC, the equivalent torsional angles are 176.7(3) and 1.7(3) ° respectively. Those for urea 1,6-dibromohexane are detailed in Table 7.…”

Section: High Pressure Studiesmentioning

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Neutron Diffraction Studies on Guest-Induced Distortions in Urea Inclusion Compounds

Lee

Mason

Mossou

et al. 2016

Crystal Growth & Design

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. (2016) 'Neutron di raction studies on guest-induced distortions in urea inclusion compounds. ', Crystal growth design., 16 (12). pp. 7175-7185. Further information on publisher's website:https://doi.org/10.1021/acs.cgd.6b01371Publisher's copyright statement:This document is the Accepted Manuscript version of a Published Work that appeared in nal form in Crystal Growth Design, copyright c American Chemical Society after peer review and technical editing by the publisher. To access the nal edited and published work see https://doi.org/10.1021/acs.cgd.6b01371. Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-pro t purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details. AbstractSingle crystal neutron structures at several temperatures have been determined for -phase urea inclusion compounds containing hexadecane, 1,6-dibromohexane and 2,7-octanedione guests. The neutron structure of the 'partial channel' co-crystal of urea and DMF is also reported. Here we present an in-depth discussion and analysis of the structure and bonding of this urea series, in particular, how the guest compound affects the symmetry and hydrogen bonding of the host urea network. Additionally, we address the challenge of obtaining crystals suitable for neutron diffraction and present a new heating/cooling device to aid crystallisation.

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The crystal structure and molecular thermal motion of urea at 12, 60 and 123 K from neutron diffraction

Cited by 295 publications

References 11 publications

Thermal properties of molecular crystals through dispersion-corrected quasi-harmonic ab initio calculations: the case of urea

Thermal properties of molecular crystals through dispersion-corrected quasi-harmonic ab initio calculations: the case of urea

Molecular electric moments and electric field gradients from X-ray diffraction data: model studies

Neutron Diffraction Studies on Guest-Induced Distortions in Urea Inclusion Compounds

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