ARTICLE pubs.acs.org/JPCB
Structural Properties of Carboxylic Acid Dimers Confined within the Urea Tunnel Structure: An MD Simulation Study Andrew J. Ilott,† Sebastian Palucha,† Andrei S. Batsanov,† Kenneth D. M. Harris,*,‡ Paul Hodgkinson,*,† and Mark R. Wilson*,† † ‡
Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, United Kingdom
bS Supporting Information ABSTRACT: Large-scale molecular dynamics simulations have been performed on solid inclusion compounds formed between urea and alkane (dodecane) and alkanoic acid (dodecanoic acid) guest molecules. The incommensurate nature of the guest and host substructures means that simulations of these systems are challenging, and our results call into question some of the simplifying assumptions made in earlier simulations on the urea inclusion compounds. Detailed information is obtained on the structural properties of the carboxylic acid dimers and alkyl chains confined within the nanoscale tunnels of the urea host structure, including the chirality of the guest conformation induced by the chiral nature of the urea tunnels. Diffusion coefficients (at 300 K) of the guest molecules along the tunnel axis were determined to be 0.091 ( 0.031 (dodecane) and 0.0063 ( 0.0013 Å2 ps-1 (dodecanoic acid), in good agreement with experimental measurements on alkane/urea systems. Weak ordering is observed between guests in neighboring tunnels, which is compatible with experimental measurements on the alkane/urea systems, although the simulations provide more detailed molecular-level insights into the nature of this supramolecular ordering.
’ INTRODUCTION Crystalline organic inclusion compounds exhibit a wide range of important physicochemical properties, and these materials represent ideal model systems for studying molecular confinement in the solid state. A prototypical family of solid organic inclusion compounds is the urea inclusion compounds,1-6 in which the host structure7,8 is constructed from a helical hydrogen-bonded arrangement of urea molecules and contains linear, parallel tunnels (see Figure 1). The tunnel diameter, which varies between ca. 5.5 and 5.8 Å as a function of position along the tunnel,9 is suitable for accommodating guest molecules based on n-alkane chains (with only a limited degree of substitution permitted). In contrast to many other types of solid inclusion compounds, such as zeolitic materials, the urea host structure is stable only when the tunnels are filled with a dense packing of guest molecules. A wide range of fundamental physicochemical aspects of urea inclusion compounds have been studied, including incommensurate structural properties,8,10-14 order-disorder phase transitions,15-20 dynamic properties (particularly concerning molecular motion of the guest molecules),21-26 properties relating to one-dimensional confinement,27-29 host-guest chiral recognition,30,31 ferroelastic properties,32,33 and transport processes.34-36 Most urea inclusion compounds have the same host structure at ambient temperature. Such “conventional” urea inclusion compounds are characterized by (i) a hexagonal host tunnel structure, (ii) an incommensurate relationship (defined below) between the periodicities of the host and guest substructures r 2011 American Chemical Society
along the tunnel direction, and (iii) substantial dynamic disorder (primarily reorientation about the tunnel axis) of the guest molecules at ambient temperature. The structural relationship between the periodicity (denoted ch) of the host structure along the tunnel and the periodicity (denoted cg) of the guest molecules along the tunnel is incommensurate if there are no sufficiently small integers m and n that satisfy the relationship: mcg = nch. The nature of incommensurate versus commensurate behavior in tunnel inclusion compounds is discussed in more detail elsewhere.10,11 The host structure involves a helical hydrogen-bonded arrangement of urea molecules, generated spontaneously during crystal growth, with a given single crystal containing either only right-handed helices (space group P6122) or only left-handed helices (space group P6522). As discussed in the Results section, the chirality of the host structure clearly has the potential to influence the structural properties of guest molecules within the tunnel. There have been a number of previous MD simulation studies of urea inclusion compounds containing alkane guest molecules,37-41 carboxylic acid guest molecules,40,42 and other types of guest.42,43 With the exception of the studies of nonadecane/urea by Souaille et al.,37-39 all MD simulations reported previously were subject to limitations imposed by one or more of the following: a rigid urea tunnel structure, a single tunnel of the Received: October 22, 2010 Revised: January 6, 2011 Published: March 10, 2011 2791
dx.doi.org/10.1021/jp110137h | J. Phys. Chem. B 2011, 115, 2791–2800
The Journal of Physical Chemistry B
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Figure 1. Snapshots of the structure in the MD simulation of dodecanoic acid/urea. (a) Viewed along the z axis of the simulation cell with the periodic boundary conditions in the x and y dimensions apparent. (b) Viewed perpendicular to the tunnel axis after an arbitrary number of time steps, showing only a single plane of molecules across two tunnels.
host structure, or a single guest molecule within the tunnel. Souaille et al. demonstrated37 that fixing the urea positions or varying cg/ch from the value observed experimentally results in simulations that poorly reproduce IQNS structure factors and hence show erroneous rates of guest diffusion and rotation. The rotational behavior is also intricately linked to the guest conformations, which are extremely sensitive to the guest packing, as also shown here (vide infra). The two previous MD simulation studies for urea inclusion compounds containing alkanoic acid guests40,42 were both subject to the limitation of a fixed urea tunnel structure. The simulation in one case42 probed only a single tunnel containing just one hydrogen-bonded alkanoic acid dimer as the guest. In the other case,40 although the simulation cell comprised nine tunnels, the host/guest ratio employed (cg/ch = 2 for dodecanoic acid guests) differs significantly from the value obtained from the X-ray diffraction studies reported here. Clearly, this fact may account for the discrepancy observed in ref 40 between the simulation results and experiment. In this work, we report new MD simulations of alkanoic acid/ urea inclusion compounds. The system considered in our MD simulation of dodecanoic acid/urea comprised nine tunnels, with a flexible host structure and a ratio of the host and guest periodicities that matches the (incommensurate) ratio determined experimentally within an accuracy of better than 0.4%. The results are seen to be highly sensitive to the quality of the simulation, helping to explain wide variations between simulations and/or experiment observed in earlier work. As now discussed, our MD simulations have yielded significant insights on a range of structural and dynamic properties of the host and guest components in these inclusion compounds. In particular, we emphasize that such simulations provide an important
opportunity to understand properties at the molecular level that, in many cases, cannot be accessed by experimental investigations. In the present work, relevant properties in this regard include the effects of confinement on the conformational properties of the guest molecules (including induced conformational properties) and detailed insights on the nature of guest-guest and guesthost interactions.
’ MD SIMULATION Our study focuses on the urea inclusion compound containing dodecanoic acid (DDA) guest molecules. For comparison, we also carried out simulations on the urea inclusion compound containing dodecane (DD) guest molecules. As a consequence of the incommensurate relationship between the host and guest substructures in these materials, the size of the simulation cell (in particular, the length of the host tunnel in the simulation cell) requires careful consideration, in order to ensure that the ratio of the host and guest periodicities along the tunnel direction is a sufficiently close approximation to its experimental value. To explore in more detail how this ratio affects the results, three further MD simulations were also carried out for DDA/urea using different values of the average periodic repeat distance of the guest molecules. The urea tunnel structure was taken from the crystal structure reported previously,8 corresponding to the P6122 form of the tunnel. In the main simulation carried out for DDA/urea (top row of Table 1), the hexagonal simulation cell comprised 171 unit cells of the host structure (1026 urea molecules) representing nine tunnels. Along the tunnel direction, the simulation cell comprised 19 unit cell repeats of the urea host structure and 6 pairs of DDA guest molecules. Thus, the (average) ratio cg/ch 2792
dx.doi.org/10.1021/jp110137h |J. Phys. Chem. B 2011, 115, 2791–2800
The Journal of Physical Chemistry B
ARTICLE
Table 1. Details of the MD Simulations guest
no. of
total no. of
no. of host unit
total no. of
no. of guest
cg/
total simulation
type
tunnels
urea molecules
cells along tunnel
guest molecules
molecules per tunnel
ch
time/ns
DDA
9
1026
19
108
12
3.17
20
DDA
9
1404
26
144
16
3.25
5
DDA
9
1458
27
144
16
3.38
5
DDA
9
1512
28
144
16
3.50
5
DD
9
432
8
45
5
1.60
10
implicit in the simulation was 19/6 = 3.17. For comparison, the repeat distance estimated from single-crystal X-ray diffraction data at ambient temperature is 35.0 ( 0.2 Å, giving a ratio of cg/ch = (35.0 Å)/(11.01 Å) = 3.18. Experimental details for the X-ray diffraction are given in the Supporting Information. The 12 molecules of DDA were placed in the tunnels as six hydrogenbonded dimers in a head-to-head/tail-to-tail arrangement, with the carboxylic acid head groups adjacent to each other to allow formation of hydrogen-bonded dimers. Both EPR44 and solidstate NMR45 measurements show that only the head-to-head/ tail-to-tail arrangement is observed for alkanoic acid/urea inclusion compounds; no signals due to head-to-tail arrangements were detected within the observability limit of
