Intermolecular Contacts in Compressed Î±-d-Mannose

Article pubs.acs.org/crystal

Intermolecular Contacts in Compressed α-D-Mannose Ewa Patyk-Kaźmierczak,† Mark R. Warren,‡ David R. Allan,‡ and Andrzej Katrusiak*,† †

Department of Materials Chemistry, Faculty of Chemistry, Adam Mickiewicz University, Umultowska 89b, 61-614 Poznań Poland Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom

‡

S Supporting Information *

ABSTRACT: The monotonic compression of α-D-mannose differs from the behaviour of all other sugars investigated so far, which all undergo phase transitions at a significantly lower pressure than the 9 GPa achieved in the current study. This exceptional stability of the α-D-mannose structure has been connected with the presence of two symmetry-independent molecules, and an increased number of degrees of freedom allowing a better accommodation of strains between hydrogenbonded molecules. The presence of C−H···O bonds accompanying the non-H-bonding O···O interactions additionally stabilizes the α-D-mannose structure.

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INTRODUCTION Even minute differences of molecular shape in isomers and similar compounds considerably affects their crystal structures.1−4 This is particularly apparent in carbohydrates.5−13 Sugars belong to the most thoroughly investigated organic compounds due to their crucial role in all living species.14 The unique sequences and positions of hydroxyl groups, which characterise each carbohydrate, govern the pattern of O−H···O bonds aggregating the molecules in crystals. Crystal structures of sugars are governed by hydrogen bonds O−H···O in a similar fashion to how they determine the structures of H2O ices. The sugar crystals and H2O ices display similar properties: they hardly change at varied temperature, but they undergo phase transitions under high pressure.15−22 Both in H2O ices and in sugars, the directional O−H···O hydrogen bonds transform when the voids present in the ambient-pressure structures collapse at high pressure. Such phase transitions were evidenced in all sugar crystals investigated as a function of pressure so far: D-sucrose,20 α-D-glucose,21 and β-D-mannose.22 The small molecular differences between isomeric α-D-glucose and its epimer, β-D-mannose, significantly affect their pressure stability. The pressure required for transforming α-D-glucose, of 5.4 GPa, is almost three times higher than 1.95 GPa transforming β-D-mannose. However, in this study no phase transitions in α-D-mannose was detected up to 10 GPa at least. This most intriguing stability achieved through the position of only one hydroxyl group repositioned between β- and α-Dmannose has been presently investigated. α-D-Mannose is exceptional among sugars in having two symmetry-independent molecules in its crystal structure and it is the only known hexose crystallizing with Z′ > 1. There are three deposited structures of simple sugars with Z′ > 1, one of them is α-Dmannose (Z′ = 2) and two others are D-ribose polymorphs (Z′ = 2 and Z′ = 3).23 However, these two D-ribose crystals inherently consist of mixed α and β anomers. In this respect α© XXXX American Chemical Society

D-mannose is a unique pristine single anomer with Z′ > 1. It also easily yields good quality single crystals suitable for highpressure studies. The pressure effect on a crystal with Z′ > 1 is still not understood. It was found that high pressure can either reduce Z′,24 stabilize the same Z′ number,25,26 or can even increase Z′.25,27,28 In the structure of α-D-mannose there are highly favored O−H···O bonds and tightly matching molecular shapes of independent molecules incompatible with any crystallographic symmetry elements. Such a tight arrangement can be resistant to compression; however, in α-D-mannose there are also short non-H-bonding O···O contacts, which potentially destabilize the structure and can result in structural transformations. These effects in compressed α-D-mannose have been investigated in this high-pressure study.

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EXPERIMENTAL SECTION

α-D-Mannose (from Sigma-Aldrich) was recrystallized from methanol:ethanol (4:1 vol.) solution. Single-crystal diffraction data were measured with a four-circle Xcalibur diffractometer equipped with sealed molybdenum X-ray tube and an Oxford Cryostream gas-flow attachment at 150, 200, 250, and 295 K (Figure S1). A Merrill-Bassett diamond-anvil cell (DAC),29 modified by mounting the anvils directly on the steel supports with conical windows, was used for high-pressure experiments. Gaskets were made of 0.1−0.3-mm-thick tungsten foil with a spark eroded 0.2−0.5 mm hole. α-D-Mannose crystals along with small ruby chips were mounted in the DAC chamber and then filled up with pentane:isopentane 1:1 (vol) mixture or saturated solution of α-D-mannose in methanol:ethanol 4:1 (vol) mixture (Figure 1). In order to fix the sample, a cellulose fiber was inserted into the DAC chamber.30 The pressure was measured with a Photon Control spectrometer, affording the 0.02 GPa accuracy. The crystals were gradually compressed and X-ray diffraction experiments were Received: July 18, 2016 Revised: October 5, 2016 Published: October 17, 2016 A

DOI: 10.1021/acs.cgd.6b01062 Cryst. Growth Des. XXXX, XXX, XXX−XXX

Crystal Growth & Design

Article

data we have excluded them from further discussion in this paper. It should be stressed that all structural models were consistent, but those based on the data measured above 9 GPa were less precise. Thus, clearly no pressure-induced phase transitions strongly reconstructing the crystal structure, like those in D-sucrose, α-D-glucose, and β-Dmannose, occur in α-D-mannose, but the compression of molecular positions, orientations, and the network of O−H···O hydrogen bonds is monotonic up to 10.13 GPa at least.

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RESULTS AND DISCUSSION Despite a reduction in volume to less than 80% of its initial value, no clear indication of phase transitions in α-D-mannose has been detected (Figure 2, Table 1 and S2). The monotonic compression is clearly nonlinear up to about 5 GPa, which coincides with the contraction of intermolecular voids (Figure 2 and S4, Table S7). The crystal is compressed strongest along a, then b and least along c, consistently with the sequence of lengths of the lattice constants. The length of parameters is

Figure 1. Single crystals of α-D-mannose at (a) 4.0 GPa (shown in polarized light) and (b) 9.6 GPa; cellulose fibers used to fix samples positions as well as small ruby chips (a) and a ruby sphere (b) for the pressure calibration, are also visible. performed at 0.50, 1.00, 1.61, 2.16, 2.49, 3.00, 3.42, 4.00, 4.39, 4.71, 4.84, 5.38, and 5.55 GPa with four-circle KUMA diffractometer and graphite monochromated MoKα radiation. Samples were centered according to previously described method.31 Additional measurements at 6.63, 8.01, 8.29, 8.60, 8.77, 9.0, 9.20, 9.37, 9.54, and 10.13 GPa were performed at the Diamond Light Source with synchrotron radiation and a four-circle Newport diffractometer equipped in a Pilatus 300 K detector. Only the best quality data, collected at 8.29, 8.60, 8.77, and 9.0 GPa, were used for structural refinements and analyses, while the other synchrotron data were used for measuring the unit-cell dimensions only. Program CrysAlisPro v. 171.38.4132 was used for the data collection, reduction, and UB-matrix determination. The structure reported by F. Longchambon et al.13 was used as the starting model for the least-squares refinement with SHELXl.33 Hydrogen atoms were positioned according to the idealized molecular geometry, with Uiso = 1.2Ueq and Uiso = 1.5Ueq for carbon and oxygen carriers; with the O− H and C−H lengths of 0.82 Å for hydroxyl groups and 0.97 or 0.98 Å for secondary or tertiary carbon atoms, respectively. The independent α-D-mannose molecules have been denoted A (atomic labels C1−C6) and B (C1′−C6′). Detailed crystallographic information is listed in Tables S1 and S2 in Supporting Information. The crystal structures of α-D-mannose have been deposited with the Cambridge Crystallographic Data Centre (CCDC1488039−1488055; 1488057−1488060; 1488073−148878) and with Crystal Open Database (3000056− 3000076, 3000080−3000085). Copies of the data can be obtained, free of charge, by filling online the application form at https://summary. ccdc.cam.ac.uk/structure-summary-form and from http://www. crystallography.net/cod/, respectively. Compressibility parameters βx = −1/x ∂x/∂p (x represents the measured unit-cell dimensions V, a, b, c, and distances between mannose rings centroids) have been calculated of the fitted exponential decay polynomials (Figures S2, S3, Tables S3−S6). Intermolecular interactions have been analyzed for the structures with C−H and O−H bonds normalized to the neutron-determined distances of 0.97 Å for oxygen atoms, and 1.098 and 1.091 Å for tertiary and secondary carbon atoms, respectively, according to Allen and Bruno.34 Contacts have been classified as hydrogen bonds O−H··· O for distances O···O shorter than 3.04 Å (i.e., the sum of van der Waals radii35); as the C−H···O bonds for distances H···O shorter than 2.72 Å and C−H···O angles higher than 110°;35,36 and as the H···H contacts for distances shorter than 2.4 Å.35 The structures at 4.39, 4.71, and 4.84 GPa were excluded from the analysis due to their poor quality and low data/parameter ratios. We observed a considerable decrease of the number of reflections starting above 9 GPa, which could be due to a partial amorphization or radiation damage of the sample. It was observed that the number of reflections and resolution constantly decreased after each measurement, i.e., with the exposition to the synchrotron radiation, even when pressure was lowered to 8.01 and 6.63 GPa. This strongly suggests that the decreased intensity of reflections is rather due to the radiation damage than pressure effect. Because of the lowered reliability of these

Figure 2. Compression of α-D-mannose crystal: (a) molecular volume (V/Z, black) and corresponding voids volume (per one molecule, purple); (b) unit-cell parameters. Empty circles represent values obtained for low-quality measurements (due to the damaged sample by synchrotron radiation). The voids volume was calculated with Mercury,37 for the probe radius and grid spacing of 0.4 and 0.1 Å (dotted lines), as well as 0.2 and 0.1 Å, respectively (dashed lines). B



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Table 1. Selected Data for α-D-Mannose Crystal at 0.1 MPa and 9.00 GPa, All at 295 Ka

a

Pressure (GPa)

0.0001

9.00(2)

Crystal system Space group a (Å) b (Å) c (Å) Volume (Å3) Z Dx (g cm−3) Final R1 (I > 4σI)

Orthorhombic P212121 23.432(3) 9.443(1) 6.884(1) 1523.0(3) 8 1.571 0.0857

Orthorhombic P212121 21.025(2) 8.762(1) 6.539(1) 1204.7(11) 8 1.987 0.0533

H8···O2′(1546) expands in the whole pressure range. Thus, this H-bond remains bifurcated, but with the lengths of distances reversed. On average the C−H···O bonds are compressed twice as much as the O−H···O bonds. Consequently, some of C−H···O bonds become comparable to ambient-pressure O−H···O bonds (Figure 4). The number of C−H···O contacts after compression to 9 GPa increases from 3 to 18, significantly more than for hydrogen bonds O−H···O, i.e., from 10 to 12. The shortest bond C1−H1···O3′(3546) with its distances H1··· O3′ of 2.03 Å and C1···O3′ of 2.67 Å coexists with a very short contact O1···O3′(3546). It is remarkable that two other non-Hbonding O···O contacts present in α-D-mannose are similarly accompanied by interactions with a CH group pushed between the two oxygen atoms: contact O6′···O4(2564) by bond C5′− H5′···O4(2564); and O5′···O5(1564) by C1′−H1′··· O5(1564), both compressed by about 0.4 Å (Figure 4a,c). Bond C5′−H5′···O4(2564) fulfills the criteria of C−H···O bond only above 8.2 GPa, when the O6′···O4 contact is compressed to about 3.04 Å. In previously investigated carbohydrates non-H-bonding O···O contacts are present in Phase I of D-sucrose, in both phases of α-D-glucose and in Phase II of β-D-mannose. However, there are some O···O contacts without any C−H···O bonds around. Two C−H···O bonds in β-D-mannose Phase I are eliminated and replaced by one O···O contact in Phase II. In α-D-glucose Phase I of two O···O contacts only one is accompanied by a C−H···O bond; however, it is long, hardly compressed, and finally breaks at the phase transition. When molecules rearrange at Pc the other O···O contact of Phase I, replaced in Phase II by a new non-H-bonding O···O contact, accompanied by a C−H···O bond common for both phases. In D-sucrose the phase transition eliminates all non-H-bonding O···O contacts despite that in Phase I these oxygen atoms are also involved in C−H···O bonds, gradually shortened with pressure. In α-D-mannose the two independent molecules form an interesting pattern where each molecule A is coordinated by six molecules B and vice versa (Figures 5, 6, and S13). The six first-

cf. Tables S1 and S2 in Supporting Information.

usually inversely proportional to the energy of cohesion forces in these directions, which agrees with the observed compressibility of α-D-mannose (cf. Figure S2 in Supporting Information). In α-D-mannose the independent molecules A and B differ in the conformation and interactions (Figures 3, 4 and S5−S12; Tables S8−S12). The largest difference in torsion angle C5− C6−O6−H12 (57.6° vs −143.8°) involves the flexible methylene C6H2 and hydroxyl O6H located in different crystal environments (Figures S5 and S7). The O−H···O bonds of independent molecules are mapped in Figure 3. In total, there are 14 independent O−H···O hydrogen bonds. Each of the ten hydroxyl groups is the H-donor in at least one O−H···O bond, and there are four bifurcated bonds, one formed by a hydroxyl group of molecule A and three by molecule B (Figures 3, S8). Each molecule A and B accepts 7 H-bonds. The compression of hydrogen bonds O−H···O, non-Hbonding contacts O···O (Figure 4), as well as other contacts becoming shorter than the sums of van der Waals radii within the pressure range investigated, varies considerably. The O···O distances in shortest O−H···O bonds are compressed by about 0.2 Å, and the longest bond O1′−H8′···O5′(2575) is compressed by ca. 0.6 Å at 9 GPa. While bond O1−H8··· O5′(1546) compress by 0.5 Å, its bifurcated counterpart O1−

Figure 3. Independent molecules A and B of α-D-mannose with O−H···O bonds involving H-donors marked in green as well as short non-Hbonding O···O contacts (shown for both oxygen atoms involved) indicated as dashed purple lines. ORTEP symmetry codes38 are explicitly explained in Table S13 (Supporting Information). C



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Figure 4. Pressure dependence of (a) O···O and (b) H···O distances for O−H···O hydrogen bonds as well as (c) C···O and (d) H···O distances for C−H···O contacts in compressed α-D-mannose. Horizontal dashed red lines mark the sums of van der Waals radii for O···O, C···O, and H···O atoms, of 3.04, 3.22, and 2.72 Å, respectively. The solid lines guide the eye for H-bonds where molecule A is the H-donor and the dashed lines for Hdonating molecule B. Non-H-bonding O···O are marked with dotted lines.

Figure 5. Pressure dependence of distances from the centroids of central molecules A (a) and B (b) to all centroids closer than 12 Å around in α-Dmannose (Table S14). Distances A···A and B···B are marked with solid lines, while dashed lines represent distances A···B/B···A. The description of the molecules involved and symmetry transformations is included in the extended version of these plots in Figure S13 in the Supporting Information. Each dashed line represents one intercentroid distance, while solid lines two or four (the red solid line) such distances.

D



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H2O ices, all undergoing pressure-induced phase transitions. It appears that the unique (for this group of compounds) structural feature of α-D-mannose, its two independent molecules, can promote the continuous compression and prevent discontinuous transformations of the crystal. The increased number of degrees of freedom of independent molecules can accommodate the strains in O−H···O hydrogen bonds. As in the other carbohydrates, the C−H···O bonds become increasingly important compared to the hydrogen bonds O−H···O. In α-D-mannose we have observed C−H···O contacts accompanying the non-H-bonding O···O short contacts and similar effects of C−H···O bonds have been identified in previously studied sugars. So far α-D-mannose is a unique example confirming this conclusion for the structures with directional O−H···O bonds as the main cohesion forces.

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ASSOCIATED CONTENT

S Supporting Information *

The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.cgd.6b01062. Detailed experimental and structural data, including temperature and pressure dependence, crystallographic data, exponential decay functions, torsion angles, bond geometry, and ORTEP symmetry codes (PDF) Accession Codes

CCDC 1488039−1488055 and 1488057−1488060 and contain the supplementary crystallographic data for this paper. These data can be obtained free of charge via www.ccdc.cam.ac.uk/ data_request/cif, or by emailing [email protected], or by contacting The Cambridge Crystallographic Data Centre, 12, Union Road, Cambridge CB2 1EZ, UK; fax: +44 1223 336033.

Figure 6. Coordination schemes (a) of α-D-mannose molecules A and B (hydrogen atoms are omitted for clarity); and (b) their centroids forming interweaved octahedral schemes at 9 GPa. The central molecules with C atoms gray and O atoms red are each surrounded by six coordinating molecules colored according to the code of distances in Figure 5 and S13. Symmetry transformations indicated by the ORTEP codes are explicitly listed in Table S13. The coordination schemes of molecules A and B, as well as the distances (in Å) between centroids, are distinguished by green and red colors. Vertices of the octahedral are colored as the corresponding molecules in Figure 6a.

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AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. Phone: +48 618291590. Fax: +48 618291555. Notes

The authors declare no competing financial interest.

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shell molecules B around molecule A form a distorted octahedron, and six closest neighbors around molecule B are molecules A forming an octahedron, too (Figure 6b). When the distances between molecular centroids are considered, there are thirteen molecules within 8 Å radius around each asymmetric molecule (Figure 5). Except for the six closest molecules shown in Figure 6, there are seven other contacts, either A···A, B···B, or A···B/B···A, complementing the coordination sphere. Similarly, for molecules A and B their first coordination shells of up to 6.5 Å between molecular centroids are compressed to below 6 Å at 9 GPa (Figure 5), and the second shells of seven molecules (A and B) below 8 Å at 0.1 MPa are compressed to about 7 Å at 9 GPa. Thus, both molecules A and B are similarly coordinated by thirteen molecules, which is close to the coordination number equal to twelve in densely packed spheres.39

ACKNOWLEDGMENTS This study was partially supported by grant START from the Foundation for Polish Science. We are grateful to Ms. Michalina Anioła and Wielkopolskie Centrum Zaawansowanych Technologii as well as to Ms. Anna Jenczak for the experimental support. We are grateful to Diamond Light Source Ltd. for hosting Mrs. Ewa Patyk-Kaźmierczak as a part of ERASMUS+ internship.

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REFERENCES

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CONCLUSIONS The crystal of α-D-mannose has been compressed monotonically up to the highest hydrostatic pressure ever applied to any sugar. It contrasts with the O−H···O bonded crystals of other sugars, D-sucrose, α-D-glucose, and β-D-mannose, as well as E



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Intermolecular Contacts in Compressed Î±-d-Mannose

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