Singularities in Molecular Conformation - Crystal Growth & Design

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Singularities in molecular conformation Szymon Sobczak, and Andrzej Katrusiak Cryst. Growth Des., Just Accepted Manuscript • DOI: 10.1021/acs.cgd.5b01156 • Publication Date (Web): 11 Oct 2015 Downloaded from http://pubs.acs.org on October 12, 2015

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Crystal Growth & Design

Singularities in molecular conformation Szymon Sobczak and Andrzej Katrusiak Department of Materials Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland. KEYWORDS molecular conformation, disorder, compression, high pressure

ABSTRACT The intramolecular coupling between molecular groups leads to singularities in the molecular conformation, acting like a switch in a molecular-scale rotor. This, in turn, affects the potentialenergy (Ep) barriers, acquiring a sharp shape originating from superimposed Ep functions of the molecular conformers with differently coupled methyl groups. The molecular conformation fixed at the switching position results in the disordered methyl orientations in the crystalline state. These general features have been observed for the molecule of pinacolone. The structure of the pinacolone crystals frozen at low-temperature isobaric and high-pressure isochoric conditions have been determined.

Introduction. Molecular-scale devices are intensely sought because of their potential applications in smart multifunctional materials, micro-robots and in medicine. Here we describe the smallest switch in

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the molecule of pinacolone (Figure 1). Its geared methyl groups induce conformational singularities of torsion angle O1=C2-C3-C4 (τ) at n·120° (n=0,1,2). For the full rotation about the central C2-C3 bond there are six potential-energy (Ep) minima at τ=n·120°±14°, three discontinuous Ep barriers at τ=n·120° and three continuous Ep barriers τ= n·60°±14°. The discontinuous and continuous Ep barriers coincide with the molecular Cs-symmetric transformations at the torsion angles τ=n·60°, consecutively at the coupled and decoupled positions of the methyl groups, respectively. The conformation of the isolated pinacolone molecule has been determined by quantum-mechanical calculations and experimentally in the crystal. We have grown single crystals of pinacolone (mp 220.65 K) in situ by isobaric, isothermal and isochoric freezing and we have solved and refined their structure by X-ray diffraction at six temperatures down to 100 K and two pressure points up to 1.56 GPa. In the crystalline state the coupling of methyl groups results in disordered acetyl H-atoms, corresponding to a molecular switch trapped in its two positions. Pinacolone is the product of pinacol rearrangement,1 one of text-book reactions in organic chemistry. Pinacolone products have manifold applications, including advanced fungicides (e.g. Triadimefon and Triadimenol)2 and as a photo-sensitizer, e.g. inter alia in an inclusion compound with deoxycholic acid, allowing the chemical storage of solar energy.3 The molecule of pinacolone is flexible, however this structure, conformation and interactions in the crystalline state have not been investigated. The pinacolone molecule involves five rotors, four of which are the methyl groups and one, about the central C2-C3 bond (Figure 1), positions the tertbutyl with respect to the acetyl group. In this study we have investigated by computational methods the conformational preferences of isolated pinacolone molecule and we have experimentally determined its structure in the crystal, where the molecular conformation is subjected to external


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stimuli modifying the crystal packing and affecting the relatively weak intermolecular CH···O interactions.

Figure 1. The structural formula of pinacolone as well as its molecule, as present in the crystal at 296 K/640 MPa with one methyl group, C1H3, disordered in two orientations about the C1-C2 bond. Torsion angle O1=C2-C3-C4 (τ) indicated in green in the formula, is equal to 0° in the crystal structure.

Experimental. Pinacolone (3,3-dimethyl-2-butanone, mp 220.65 K at ambient pressure4,5) of 98% purity from Sigma-Aldrich, was used as delivered. Liquid pinacolone was loaded into a modified MerrillBassett6 diamond-anvil cell (DAC), with diamond anvils mounted directly on steel supports with conical windows. The gasket was made of stainless steel 0.3 mm thick, with a hole 0.4 mm in diameter. The freezing pressure of pinacolone at 0.49 GPa at 296 K has been determined from an


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anomaly in the compression (Figure S3), measured in a piston-and-cylinder press.7 Two single crystals of pinacolone were grown in situ in the DAC: one near the freezing point at 0.64 GPa (Figure 1) and the other at 1.52 GPa. No hydrostatic fluid was added, as at each pressure point the crystal was grown and annealed to avoid its strain. Pressure was calibrated using the rubyfluorescence method and a Photon Control spectrometer8 affording the accuracy of 0.03 GPa. The X-ray diffraction data were measured on a KUMA4-CCD diffractometer (MoKα radiation from a sealed tube). The DAC was centered by the gasket-shadow method.9 For data collections and initial data reduction the CrysAlisPro 171.37.31 software was used. The DAC absorption, gasket shadowing and the sample absorption were calculated with program Redshabs.10 The structure was solved by direct methods (SHELXS) and refined with SHELXL;11 the Olex2 interface was used.12 Apart from the diffractometric measurements (Table 1), the molecular

Figure 2 Pinacolone single crystal grown in situ in a diamond-anvil cell in isochoric conditions at (a) 393 K; (b) 362 K; (c) 348 K; and (d) 296 K/ 0.64 GPa. The ruby chip for pressure calibration lies at the upper-left part of the chamber. The Miller indices of crystal faces have been indicated (b). ACS Paragon Plus Environment

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volume (Vm) of pinacolone (including its liquid phase, Figure S2) was measured in a piston-andcylinder press.7 The initial volume (Vo) of the pressure chamber was 9.5 ml and formula Vm=Vo/(nmNA) was applied, where nm is the number of moles and NA is the Avogadro number. The low-temperature data were measured on the same KUMA4-CCD diffractometer equipped a gas-flow Oxford Cryostream attachment. A drop of pinacolone was frozen in situ in a glass capillary, 0.3 mm in diameter, and then temperature was cycled about the mp to melt nearly all the sample and freeze it again, until a single crystal grew of all the drop. The H-atoms were located from the molecular geometry, refined and then compared with the location of peaks in the difference Fourier maps. In all the maps additional peaks appeared around methyl group C1H3 and therefore its disorder has been assumed. We have retained the constrained geometry of the methyl group, but allowed its rotations about the C1-C2 bond. Consequently, the orientation of this methyl group was not restricted by the crystal symmetry of the mirror plane, and two halfoccupied sites of the methyl group were generated (Figure 1). The R factors were markedly reduced by the C1H3 group disordered and therefore it has been included in the structural final model. The selected crystal data are listed in Table 1; the experimental and structural details are given in the Supplementary Table S1 and have been deposited in the Cambridge Crystallographic Database Centre (numbers: CCDC 1030727-1030734). Copies can be obtained free of charge from pubs.acs.org. The pinacolone molecule was fully optimized for the τ angle changed in steps of 1 degree between -30° and 75°. Theoretical computations of the density-functional and post-Hartree-Fock methods with program Gaussian13 were performed at the B3LYP/aug-cc-pVTZ14, LC-ωPBE/aug-


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cc-pVTZ15, and MP2/aug-cc-pVTZ16, levels of theory. These theoretical and experimental methods yield consistent results, which have been explained below.

Table 1. Selected high-pressure crystallographic data of pinacolone Pressure

0.1 MPa

0.64 GPa

1.52 GPa

Temperature

100 K

296 K

296 K

Space group

P21/m

P21/m

P21/m

a [Å]

5.6780(9)

5.684(3)

5.521(12)

b [Å]

8.6234(15)

8.5670(6)

8.3045(5)

c [Å]

6.9697(11)

6.8598(8)

6.716(2)

β [°]

108.215(17)

107.97(3)

107.89(11)

Volume [Å3]

324.16(9)

317.89(17)

293.0(6)

Z/Z’

2/0.5

2/0.5

2/0.5

Dx [g/cm3]

1.026

1.047

1.135

Discussion The highest symmetry Cs possible for the pinacolone molecule requires that torsion angle τ (Figure 1) be either equal to n·120° (n=0,1,2) or 60°+n·120° for two distinctly different conformations, one with the carbonyl coplanar with one of tertbutyl methyls (τ=0°), and the other when the carbonyl is staggered (τ=60°). Our survey of the Cambridge Structural Database (Version 5.36) revealed 7 solvate crystals with 11 independent pinacolone molecules. In 3 crystals the τ angle is in the 0-5° range, in 3 structures between 5-15º, and in 4 structures in the range from 15 to over 30°.3,17-22 In the co-crystal with deoxycholic acid angle τ is the highest, of


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30.05°, which is considered essential for its photosensitizing effect.3 The conformation of pinacolone, apart from torsion angle O1=C2-C3-C4 (τ. Figure 1), involves the rotations of methyl groups C1H3, C4H3, C5H3 and C5’H3. Torsion angle τ depends on the interplay of molecular electronic effects, such as a hyperconjugation between the carbonyl and methyl groups, intramolecular non-bonding forces and steric hindrances. The intramolecular effect of hyperconjugation, coupling the π-electrons of carbonyl C=O with σ-electrons of bond C3-C4, favors the planar conformation of the O1=C2-C3-C4 bonds system, as well as some lengthening of bond O1=C2 and shortening of bonds C2-C3 and C3-C4. The intramolecular hindrances in pinacolone involve mainly the methyl groups at C2 and C3, and favor the staggering of methyl C1H3 between C5H3 and C5’H3. Finally, the intramolecular electrostatic interactions between hydrogen atoms at C4H3 and the electronegative oxygen O1 favor the planar conformation i.e. torsion angle τ=0°, when assuming the methyl H-atoms ideally staggered with respect to the C-C bonds. Our theoretical computations of the molecular energy Ep as a function of torsion angle τ (Figure. 3), with all other molecular dimensions freely optimized, are consistent with the conformational effects described above. However, the acute peak of the Ep barrier at 0° clearly differs from the Gaussian-function shape of typical Ep barriers. The calculations repeated at various levels of theory reproduced the acute barrier shape (Figure 4) and we have concentrated on explaining this exceptional feature. The highest Ep barrier, ∆E1, of about 3 kJmol-1, (according to the most accurate calculations, plotted in Figure 4) is at τ=60º, when torsion angle C1-C2-C3C5 (or equivalent C1-C2-C3-C4 and C1-C2-C3-C5’) is 0º and the steric hindrances between the methyls are the strongest (Figure 4). The shape of this barrier is typical, with a rounded peak. The Ep minima occur at six equivalent τ angles (0±14)°, (120±14)° and (240±14)°, while the τ=0º is associated with the sharp Ep barrier of about 1 kJmol-1. It occurs when torsion angle τ


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passes through 0°, which implies the rotation of methyl C1H3 by ∆τ5=60° and that this abrupt conformation change is coupled to small abrupt rotations of the methyl hydrogen atoms at the closely located groups C5H3 (τ3) and C5’H3 (τ2). These rotations relax the steric hindrances due to the overcrowding of the H-atoms, and they cumulate in the largest rotation (∆τ5) of methyl group C1H3. The rotations of methyl hydrogen atoms, in turn, are coupled to the torsion angle τ. This coupling in the molecule of pinacolone acts like a ratchet, switched over by angle τ passing through 0°. The discontinuities in the positions of the methyls can be regarded as a consequence of the symmetry relations between conformations of the transforming pinacolone molecule. The molecule acquires the Cs symmetry at τ=0° and at τ=60° (Figure 4), and the conformations on both sides of these τ values are Cs-symmetrically (mirror plane) related. In other words, they are enantiomeric pairs. The Cs relation requires that all torsion angles in the molecule change their sign. For the τ=60° all the torsion angles in the molecule, including τ2, τ3, τ4 and τ5 are very close or equal to 60° (according to our theoretical computation), and each of these torsion angles involves either equivalent methyl groups (for angle τ groups C4H3, C5H3 and C5’H3) or equivalent H atoms (for angles τ2, τ3, τ4 and τ5). This equivalence means that for each torsion angle equal to 60° there is an equivalent angle of -60°. Thus the possible transformation between enantiomeric points can proceed continuously, because the requirement of reversed sign of torsion angles is fully fulfilled.


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When the molecular conformation transforms through the sharp Ep barrier at τ =0°, the requirement of reversed signs can be smoothly fulfilled for τ2, τ3, and τ4, however for torsion angle τ5=-30° for the positive τ approaching 0° there are no equivalent H atoms in methyl C1H3 at the opposite τ5 value, of positive sign at τ5=30°, when τ passes through 0° and becomes negative. Therefore, in accordance with the Cs-symmetry requirements, torsion angle τ5 should increase by 60° to the 30° value. This strong discontinuous rotation is accompanied by weaker discontinuities in τ2, τ3 and τ4, which are coupled to τ5. Angles τ2, τ3 and τ4 are all close to 60° when τ passes through 0°.

Figure 3. Potential energy change (∆Ep) of the molecule calculated at the MP2/cc-pVTZ level of theory as a function of torsion angle τ (O1=C2-C3-C4). The minimum of potential energy occurs at 14°±n·120°. Red dashes indicate the torsion angles of pinacolone molecules present in co-crystalline compounds.

3,17-22

The ∆Ep barriers have been indicated and the inset (top)

expands the schematic ∆Ep to over one full rotation of the tert-butyl group.


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The sharp peaks of Ep(τ) passing through 0, 120 and 240° is consistent with our solid-state structural studies. In the crystal structure (Figure S1) molecules lie on the mirror planes. This conformation with the τ angle equal 0º results of symmetric crystal environment: intermolecular packing forces and the lattice modes of vibrations favoring the Cs-symmetric lattice. The

Figure 4 Potential energy changes (∆Ep) and conformation of the pinacolone molecule (torsion angles τ2, τ3, τ4 and τ5 are indicated in the inset in the bottom plot – the larger version of this drawing is shown in Supplementary Figure S10) fully optimized as a function of torsion angle τ in the theory levels MP2/ LC-ωPBE/ B3LYP/aug-cc-pVTZ. Pinacolone molecules in the Newman projection are shown in the upper plot. disordering of the C1H3 methyl orientation confirms its ratchet-type coupling with angle τ


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passing 0° (cf. Figure 4). It appears that the rotation of methyl C1H3 minimizes its steric hindrances with symmetry equivalent methyl groups C5H3 and C5’H3. Two sites of the disordered methyl group C1H3 correspond to two Ep(τ) functions, each of them corresponding to the methyl groups rotated in the opposite sense.

Figure 5 Thermal expansion (left) and compression (right) of pinacolone, in relation to the average unit-cell dimensions (ao, bo, co, Vo) calculated of the highest-temperature ambientpressure (200 K/0.1 MPa) and room-temperature lowest-pressure (296 K/0.49 GPa) data. The shaded region indicates the liquid phase between 202.2 K/0.1 MPa and 296 K/0.49 GPa, and the temperature and pressure units have been scaled to obtain the same width of the liquid phase. Our differential scanning calorimetry (DSC) measurements (Figure S2) show that pinacolone freezes at 220.65 K, consistently with the literature data.4,5 This crystal phase frozen at 220.65 K


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persists down to 100 K at least. The compression measured in a piston-and-cylinder press shows that pinacolone freezes at 0.49 GPa at 296 K. In the crystalline state the thermal expansion and compression of pinacolone are all positive, and they are consistent with the reverse relationship rule of temperature and pressure effects.23 Due to the weak interactions between molecules, pinacolone is liquid at normal conditions, and its high-pressure or low-temperature freezing leads to a typical molecular crystal with the coordination number of each molecule equal to 12, characteristic to densely packed spheres and most frequent for the molecular crystals.24 The inspection of all intermolecular contacts show that they are longer or only very slightly shorter than the sum of van der Waals radii. Figure 5 shows that the shortest contacts gradually contract at low temperature and are similarly compressed, but at a stronger rate.

Figure 6 Shortest intermolecular contacts in pinacolone plotted as a function of temperature (left) and pressure (right). The lines joining the points are for guiding the eye only. The horizontal dashed lines indicate the sums of van der Waals radii.25


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Conclusions. The sharp Ep barrier at τ=0° in the isolated pinacolone molecule can be associated with the intramolecular steric hindrances and geared rotations of hydrogen atoms of overcrowded methyl groups. This acute type of the Ep barrier is the consequence the superposition of two independent Ep(τ) functions, each associated with one of two possible orientations of the coupled methyl groups. In the crystal, the exactly aligned acetyl group with one of tertbutyl methyls is consistent with the special Cs-symmetric position of molecules and their symmetric environment. However, this is the τ=0° switching position for the coupled overcrowded methyl groups, which results in the acetyl-methyl hydrogen trapped and disordered in two orientations. The molecular conformation geared to the orientation of other molecular fragments can constitute elements applicable for constructing larger molecular-scale devices and multifunctional materials. We have found reports with, acute Ep barriers in the molecules of functional materials, although their origin was not explained.26 It appears that the effects of coupling between molecular substituents can be rationally used for constructing the elements of machines at the molecular level.27-30 Acknowledgments. We are grateful to Ms. Kinga Ostrowska, Ms. Ewa Patyk, Mr. Michał Andrzejewski, Mr. Jędrzej Marciniak and Mr. Damian Paliwoda of the Department of Materials Chemistry, Faculty of Chemistry, Adam Mickiewicz University for support and advices. The theoretical computations in Poznań Supercomputing and Networking are gratefully acknowledged.


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For Table of Contents Use Only Singularities in molecular conformation Szymon Sobczak and Andrzej Katrusiak*

The molecular switch of pinacolone molecule involves geared methyl groups, leading to their discontinuous repositioning for torsion angle O1=C2-C3-C4 close to 0°.


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Singularities in Molecular Conformation - Crystal Growth & Design

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