Predicting anisotropic displacement parameters using molecular dynamics: density functional theory plus dispersion modelling of thermal motion in benzophenone

Reilly, Anthony M.; Wann, Derek A.; Gutmann, Matthias J.; Jura, Marek; Morrison, Carole A.; Rankin, David W. H.

doi:10.1107/s0021889813006225

Cited by 15 publications

(4 citation statements)

References 49 publications

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“…The X-ray dataw ere refined in the triclinic space group P1 with the whole molecule occupying the asymmetric unit. The coordinating bp ligand has aC ÀOb ond length of 1.236 (1) , which is nearly identical with that of free bp, [24] indicating that the C=Ob ond is barely affected by complexation. Although the outcomec ontrasts that of the reactiono f[ Yb(DippForm) 2 (thf) 2 ]w ith Ph 2 CO, where aC ÀCc oupled product was obtained in good yield, [11a] [Yb(DF-Form) 3 (bp)] was only obtained in low yield and cannot be the sole product.…”

Section: Oxidation Of [Yb(dfform) 2 (Thf) 3 ](Yb3)mentioning

confidence: 94%

Enhancing the Value of Free Metals in the Synthesis of Lanthanoid Formamidinates: Is a Co‐oxidant Needed?

Deacon

Junk

Werner

2015

Chemistry A European J

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Treatment of N,N'-bis(aryl)formamidines (ArFormH), N,N'-bis(2,6-difluorophenyl)formamidine (DFFormH) or N,N'-bis(2,6-diisopropylphenyl)formamidine (DippFormH), with europium metal in CH3 CN is an efficient synthesis of the divalent complexes: [{Eu(DFForm)2 (CH3 CN)2 }2 ] (Eu1) or [Eu(DippForm)2 (CH3 CN)4 ] (Eu2). The synthetic method was extended to ytterbium, but the metal required activation by addition of Hg(0) . With DFFormH in CH3 CN, [{Yb(DFForm)2 (CH3 CN)}2 ] (Yb1) was obtained in good yield, and [Yb(DFForm)2 (thf)3 ] (Yb3) was obtained from a synthesis in CH3 CN/THF. Thus, this synthetic method completely circumvents the use of either salt metathesis, or redox transmetallation/protolysis (RTP) protocols to prepare divalent rare-earth formamidinates. Heating Yb1 in PhMe/C6 D6 resulted in decomposition to trivalent products, including one from a CH3 CN activation process. For a synthetic comparison, divalent ytterbium DFForm and DippForm complexes were synthesised by RTP reactions between Yb(0) , Hg(R)2 (R=Ph, C6 F5 ), and ArFormH in THF, leading to the isolation of either [Yb(DFForm)2 (thf)3 ] (Yb3), or the first five coordinate rare-earth formamidinate complex [Yb(DippForm)2 (thf)] (Yb4 b), and, from adjustment of the stoichiometry, trivalent [Yb(DFForm)3 (thf)] (Yb6). Oxidation of Yb3 with benzophenone (bp), or halogenating agents (TiCl4 (thf)2 , Ph3 CCl, C2 Cl6 ) gave [Yb(DFForm)3 (bp)] or [Yb(DFForm)2 Cl(thf)2 ], respectively. Furthermore, the structural chemistry of divalent ArForm complexes has been substantially broadened. Not only have the highest and lowest coordination numbers for divalent rare-earth ArForm complexes been achieved in Eu2 and Yb4 b, respectively, but also dimeric Eu1 and Yb1 have highly unusual ArForm bridging coordination modes, either perpendicular μ-1κ(N:N'):2κ(N:N') in Eu1, or the twisted μ-1κ(N:N'):2κ(N':F') DFForm coordination in Yb1, both unprecedented in divalent rare-earth ArForm chemistry and in the wider divalent rare-earth amidinate field.

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Section: Oxidation Of [Yb(dfform) 2 (Thf) 3 ](Yb3)mentioning

confidence: 94%

Enhancing the Value of Free Metals in the Synthesis of Lanthanoid Formamidinates: Is a Co‐oxidant Needed?

Deacon

Junk

Werner

2015

Chemistry A European J

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“…By contrast, R -Diastereoisomer-2 adopts a less bent saddle-shaped conformationwhich can be obtained from R -Diastereoisomer-1 by rotating the two diagonal outwardly inclined phenylene rings through 180°wherein two phenylene rings in each benzophenone moiety are in an anti orientation, with a “dihedral angle” of 49° and a distance between the two ketonic CO groups of 5.2 Å. The torsional angles (Table S1) at comparable locations in the benzophenone units in R -Diastereoisomer-2 are quite similar to those in the solid-state structure of pristine benzophenone but rather different from the torsional angles of R -Diastereoisomer-1 . In the single-crystal superstructure, R -Diastereoisomer-1 and R -Diastereoisomer-2 are engaged together through their concave faces to form a supramolecular dimer by means of a [C–H···O] hydrogen-bonding interaction ( d H···O = 2.38 Å and θ C–H···O = 166°) between an H atom on one of the outwardly tilted phenylene rings of R -Diastereoisomer-2 and an inwardly pointed O atom on one of the imide groups of R -Diastereoisomer-1 .…”

Section: Resultsmentioning

confidence: 98%

Supramolecular Double-Helix Formation by Diastereoisomeric Conformations of Configurationally Enantiomeric Macrocycles

et al. 2016

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Solid-state superstructures, resulting from assemblies programmed by homochirality, are attracting considerable attention. In addition, artificial double-helical architectures are being investigated, especially in relation to the ways in which homochiral small molecules can be induced to yield helical forms as a result of chiral induction. Herein, we report the highly specific self-assembly upon crystallization of a double-helical superstructure from an enantiopure macrocyclic dimer which adopts two diastereoisomeric conformations in a molar ratio of 1.5:1 in dimethyl sulfoxide. These two conformational diastereoisomers self-organize-and self-sort-in the crystalline phase in equimolar proportions to form two single-handed helices which are complementary to each other, giving rise to the assembly of a double helix that is stabilized by intermolecular [C-H···O] and π-π stacking interactions. The observed self-sorting phenomenon occurs on going from a mixed-solvent system containing two equilibrating conformational diastereoisomers, presumably present in unequal molar proportions, into the solid state. The diastereoisomeric conformations are captured upon crystallization in a 1:1 molar ratio in the double-helical superstructure, whose handedness is dictated by the choice of the enantiomeric macrocyclic dimer. The interconversion of the two conformational diastereoisomers derived from each configurationally enantiomeric macrocycle was investigated in CDSOCD solution by variable-temperature H NMR spectroscopy (VT NMR) and circular dichroism (VT CD). The merging of the resonances for the protons corresponding to the two diastereoisomers at a range of coalescence temperatures in the VT NMR spectra and occurrence of the isosbestic points in the VT CD spectra indicate that the two diastereoisomers are interconverting slowly in solution on theH NMR time scale but rapidly on the laboratory time scale. To the best of our knowledge, the self-assembly of such solid-state superstructures from two conformational diastereoisomers of a homochiral macrocycle is a rare, if not unique, occurrence.

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“…With current hardware and soware algorithms, it is feasible to perform periodic calculations on medium-sized molecular crystals (up to a few hundred atoms) using DFT with semi-local (meta-)GGA functionals, or, in some cases, with hybrids. [10][11][12][13] This is usually sufficient for studying equilibrium geometry and lattice dynamics (e.g. vibrational frequencies), but semi-local functionals are oen not able to describe electronic structure quantitatively, as is required, for example, for accurate prediction of optical properties.…”

Section: Explicit Periodic Calculationsmentioning

confidence: 99%

Electronic excitations in molecular solids: bridging theory and experiment

et al. 2015

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As the spatial and temporal resolution accessible to experiment and theory converge, computational chemistry is an increasingly powerful tool for modelling and interpreting spectroscopic data. However, the study of molecular processes, in particular those related to electronic excitations (e.g. photochemistry), frequently pushes quantum-chemical techniques to their limit. The disparity in the level of theory accessible to periodic and molecular calculations presents a significant challenge when modelling molecular crystals, since accurate calculations require a high level of theory to describe the molecular species, but must also take into account the influence of the crystalline environment on their properties. In this article, we briefly review the different classes of quantum-chemical techniques, and present an overview of methods that account for environmental influences with varying levels of approximation. Using a combination of solid-state and molecular calculations, we quantitatively evaluate the performance of implicit-solvent models for the [Ni(Et4dien)(η2-O,ON)(η1-NO2)] linkage-isomer system as a test case. We focus particularly on the accurate reproduction of the energetics of the isomerisation, and on predicting spectroscopic properties to compare with experimental results. This work illustrates how the synergy between periodic and molecular calculations can be exploited for the study of molecular crystals, and forms a basis for the investigation of more challenging phenomena, such as excited-state dynamics, and for further methodological developments.

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Predicting anisotropic displacement parameters using molecular dynamics: density functional theory plus dispersion modelling of thermal motion in benzophenone

Cited by 15 publications

References 49 publications

Enhancing the Value of Free Metals in the Synthesis of Lanthanoid Formamidinates: Is a Co‐oxidant Needed?

Enhancing the Value of Free Metals in the Synthesis of Lanthanoid Formamidinates: Is a Co‐oxidant Needed?

Supramolecular Double-Helix Formation by Diastereoisomeric Conformations of Configurationally Enantiomeric Macrocycles

Electronic excitations in molecular solids: bridging theory and experiment

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