6th International Conference on Gas Hydrates

A LOW SYMMETRY FORM OF STRUCTURE H CLATHRATE HYDRATE Ripmeester, John A.; Ratcliffe, Christopher I.; Udachin, Konstantin A. 2008

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A LOW SYMMETRY FORM OF STRUCTURE H CLATHRATE HYDRATE   Konstantin A Udachin, Christopher I. Ratcliffe, John A. Ripmeester* Steacie Institute for Molecular Sciences National Research Council Canada Ottawa, ON K1A 0R6 Canada  ABSTRACT In this paper we report a low symmetry version of structure H hydrate that results from the hexagonal form on  cooling  below  167  K.    Phase  changes  with  temperature  in  the  common  clathrate  hydrates  structural families I, II and H have not been observed before, except in doped systems where ordering transitions take place or in the structure I hydrate of trimethylene oxide where the guest molecule dipoles are known to order.  Since there is an inverse relationship between the effect of temperature and pressure on ices, it may well be that the low  symmetry  form  reported at  low  temperature  can  also  be  reached  by  applying  high pressure,  and  that  in  fact  some  of  the  observed  high  pressure  phases  are  lower  symmetry  versions  of hexagonal sH.   Clathrate  hydrates  are  crystalline  guest-host materials where small guest molecules are trapped in cages formed by hydrogen bonded molecules[1,2].  The three common families of hydrate structures, known  as  cubic  structures  I  (sI)  and  II  (sII)  and hexagonal  structure  H  (sH),  form  when  the different cage types are packed into ordered three dimensional structures. All three hydrate structures have  been  identified  as  occurring  in  nature,  with hydrocarbon guests, H2S, CO2, O2, N2 and traces of the noble gases, either offshore on the continental margins  [3,4,5],  under  the  permafrost[6],  or  deep inside glaciers[7].    Normally  methane  forms  sI  hydrate,  but  sII  has been observed as well as a transient phase[8] and at higher pressures a variety of new phases have been observed.  A  methane  hydrate  phase  that  is  either sH or close to sH in structure is known to form at high  pressure,  which  transforms  to  a  ?filled  ice?  above ~ 2 GPa[9-14].  The high pressure phases are not  known  to  occur  naturally  on  earth,  but  have been  implicated  as  perhaps  playing  a  role  on  the icy outer planets[8].   Similarly, noble gas atoms or small  molecules  that  normally  form  sI  or  sII hydrates  are  known  to  transform  to  other  hydrate structures,  including  sH  hydrate[15-20]  under application  of  high  pressure.    Hexagonal  sH  was first  identified  from  NMR  spectroscopy  and powder  neutron  data[21,22]  with  the  structure confirmed  from  single  crystal  X-ray diffraction[23,24].  We  note  that  the  high  pressure methane hydrate phase (MH-II) has been described as  not  exactly  having  the  hexagonal  clathrate structure but one that may be closely related to it, although  other  work  has  concluded  that this  high pressure phase indeed is hexagonal sH[19]. Clearly there is a great interest in the diversity of hydrate structures  and  the  conditions  under  which  these form.    In this paper we report a low symmetry version of sH  hydrate  that  results  from  the  hexagonal form[21,24] on cooling below 167 K.  Phase changes with temperature in the common clathrate hydrates structural  families  I,  II  and  H  have  not  been observed  before,  except  in  doped  systems  where ordering  transitions  take  place[25]  or  in  the  sI hydrate  of  trimethylene  oxide  where  the  guest molecule  dipoles  are  known  to  order[26].    Since there is an inverse relationship between the effect of temperature and pressure on ices, it may well be that  the  low  symmetry  form  reported  at  low temperature can also be reached by applying high pressure, and that in fact some of the observed high pressure  phases  are  lower  symmetry  versions  of hexagonal sH.  EXPERIMENTAL  sH  hydrate,  with  cyclooctane  as  the  large  cage guest  and  Xenon  and  hydrogen  sulphide  in  the small cages was confirmed to form sH some years ago[22].  The single crystal resulted upon storing a sealed sample for several years in a freezer at -40 C?.  The crystal was recovered and mounted on the diffractometer  at  low  temperatures.  Data  was collected  on  a  Bruker  Smart  diffractometer  at  a temperature  of  125K.  Integration  was  carried  out using  the  program  SAINT,  and  an  absorption correction was performed using SADABS[27].   The   Table 1.  Summary of X-ray structural data    Structure H  Structure H?           a=12.313(1)  c=10.054(1)  a=24.433(2)  c=10.010(2)  Unit - cell volume, ? 3 1320.1(1)   517 5.1(10)  Temperature, K   215.0(1)   125.0(1)  Reflections collected  14992   58779  Reflections unique  700   8551  Reflections >2?(I)                 R1  0.018   0.035  wR2  0.047   0.094  residual electron density, e? -3 max. 0.29, min.   - 0.25  max. 0.40, min.   - 0.84      structure was solved  by d irect methods and refined by  full - matrix  least - squares  routines  using  the SHELXTL  program  suite [28].  All  atoms  were refined  anisotropically.  Hydrogen  atoms  on cyclooctane  molecules  were  placed  in  calculated positions and allowed to ride on the parent atoms. Surprisingly,  the  crystal  proved  not  to  be  sH hydrate  but  a  lower  symmetry  version.  A differential  scanning  calorimetry  scan  revealed  a weak  endotherm  at  -106  C?  suggesting  the presence of a phase transition.     A second data set taken  at  -85C?,  above  the  phase  transition,  was consistent  with  the  previously  determined  sH structures  as  determined  from  previous  single crystal  studies[23,24].    A  summary  of  the  X-ray structural data is given in Table 1.  RESULTS AND DISCUSSION After the low temperature structure was discovered to  be  different  from  the  usual  hexagonal  sH clathrate, attempts were made to see if this phase was  the  stable  one  for  this  particular  large  guest molecule.  However, it was found that at -85C? the phase had transformed to the hexagonal form, and that  the  single  crystal  survives  the  phase  change.  The  transition  temperature  was  identified  to  be  -106C?  from  differential  scanning  calorimetry (fig.1).     This    is     the    first     example    of    a   Figure 1.  Differential Scanning Calorimetry traces of  the  thermal  transitions  in  sH  hydrate.    Inset shows a detail of the phase change region.  temperature-induced symmetry lowering transition in  the  lattice  of  the  common  clathrate  families.  However, such transitions are well-documented in the  silica  clathrates  that  are  isostructural  with  the water clathrates and known as clathrasils [30, 31].    The low temperature structure has a space group of reduced symmetry as compared to that determined at high temperature: P6/mmm (a= 12.313(1) ?, c= 10.054(1) ?, V = 1320.1(1) ?3, T=215K) to P3bar (a= 24.433(2) ? c=10.010(1) ? V = 5175.1(1) ?3, T=125K).  So, there  is  a  doubling  of  the  a  lattice parameter (fig.2), and the unit cell volume at low temperature     (200K)     is     exactly     the    same   Figure  2.    General  views  of  the  structures  of  sH hydrate, low and high temperature forms.  (within  the  calculated  errors)  as  the  quadrupled volume of the high temperature (206K) cell. Table 2  shows  structure  H?  and  structure  H  unit -cell parameters  and  cell  volumes  at  different temperatures.  This  is  a  good  illustration  of  the flexibility of water framework as the distortion of the  large  cages  is  compensated  by  an  equivalent distortion in the small cages.  Table  2.  Structure  H?  and  structure  H  unit -cell parameters  and  cell  volumes  at  different temperatures. Temperature, K  a  c  V 80K   24.445(2)   10.005(1)   5177(1)  100K   24.458(2)   10.007(1)   5184(1)  125K   24.496(2)   10.015(1)   5204(1)  150K   24.525(2)   10.026(1)   5222(1)  175K   24.577(2)   10.034(1)   5248(1)  200K   24.629 (2)   10.052(1)   5280(1)         206K   12.315(1)   10.056(1)   1320.8(3)  215K   12.327(1)   10.062(1)   1324.0(3)  225K   12.331(1)   10.067(1)   1325.7(3)   There  are  considerable  implications  for  the  sizes and shapes of the various cages that make up sH.The high temperature unit cell can be described as 3D.2D? .E.34H2O, where D = 512,  D?=4 35663 and E = 51268, with the cage symmetries given in table 3.  The  low  temperature  unit  cell  becomes 6Da.6Db.4D? a.4D? b.2Ea.2Eb.136H2O,  with  a considerable loss of symmetry for all of the cages.  Table  3.  Symmetry  of  the  cages  in  the  high  and low temperature forms of sH hydrate   Structure H E.3D.2D?.34H 2O   5 12(D)  4 35 66 3(D?)  126 8(E)   mmm  m2  6/mmm   Structure H? 4[E.3D.2D?.34H 2O]   5 12(D)  5 12(D)  4 35 66 3(D?)  35 66 3(D?)  126 8(E)  5 126 8(E)   1  1  1  3  - 1  - 1    The most profound effect of the structural change is on the large E cages and their guest distributions.  Fig. 3   shows that the two cages alternate along the x direction.   Both cages are   deformed and the cage located on the 3 - fold axes is disordere d over three symmetry  related  positions  with  equal  site occupancy  (fig.4).  They  both  have  symmetry  - 1. The longest and the shortest diameters within the 001 plane are 9.12 and 9.77 ? for the ordered E -cage and 9.22 and 9.64 ? for the disordered E - cage as  c ompared  to  those  in  the  high  temperature  symmetric  cage  (9.45  ?).  This  is  also  noticeable from the distribution of the cyclooctane molecule sites   in   the   cage:   in   the   low   symmetry cage the      Figure  3.    Detail  of  structure  showing  the alternating E   cages along the  x direction; the two E cages  showing  the  cage  distortions  and  the cyclooctane guest positions   Figure  4.  Disordered  E  cage  and  cyclooctane orientations  in  structure  H?  (cage  deformation  is slightly exaggerated for clarity).  favored  positions  of  the  guest  lie  along  the stretched dimension of the cage (fig.4).  We may speculate that the ability to distort the cage comes from  the  fact  that  the  cyclooctane  guest  is  quite large  and  asymmetric  (in  its  most  stable conformation).    Cyclooctane  conformations  are  approximately  the same  in  structure  H  and  in  both  large  cages  of structure H? . Cage volumes calculated at 206 K for structure  H  and  at  200  K  for  structure  H?  are approximately  the  same  (268?2?3).  The  volumes were  calculated  using  the  PLATON  program[29]. The low  symmetry  large  cages  in  structure  H?  are deformed, but have the same volume. The same is true for the small cages. Both small and large cages are deformed, but the volumes of the cages and the unit-cell  volumes  (exactly  4  times  larger  for structure H?)  remain the same.  At this time, we can only speculate on the reason for the transformation of the sH framework as the temperature  is  lowered.    The  unit  cell  and  cage volumes appear to be identical in both phases but the  loss  of  symmetry  may  offer  a  clue,  however.   In  the  high  temperature  phase,  the  cyclooctane guest is disordered over 6 positions, whereas in the low  temperature  phase  there  is  just  one  guest orientation  although  the  cage  orientations  are disordered.  Guest dynamics have not been studied in  detail  for  sH  hydrate,  but  in  at  least  one  sH system  (methylcyclohexane)  the  guest  rotates between  the  6  equivalent  positions  that  lie  about the symmetry axis of the E cage. This suggests that freezing in of guest motion in one of the equivalent   Figure  5.  Calculated  powder  X-ray  diffraction patterns for low (A) and high (B) symmetry forms of cyclooctane hydrate.  positions  in  the  large  cage  may  occur,  and  once this  happens  the  cage  distorts  to  maximize  host-guest  interaction.      Cyclooctane,  as  a  stationary molecule, departs quite markedly from cylindrical symmetry,  as  do  the  close  fitting  E  cages  in  the low temperature phase.  The transition then can be considered  to  be  driven  by  the  freezing  in  of  the motion  of  a  tightly  fitting  low  symmetry  guest, thus  distorting  the  host  cavity.  This  situation should  not  be  expected  to  be  unique  for  this particular guest.  Other large guests, or asymmetric configurations  of  small  molecules  such  as  in  the high pressure phases, may well drive sH hydrate to its  lower  symmetry  version.  We  note  that  some clathrasils,  clathrate  compounds  of  silica  and isostructural  with  the  clathrate  hydrates[29],  show progressive symmetry lowering as the temperature is  lowered,  implicating  restricted  guest  dynamics and symmetry lowering of the host lattice[30]. We also note that it is not possible to distinguish the low and high symmetry forms by powder X-ray diffraction,  as  the  patterns  are  exactly  the  same (fig.5).       [1]    G.  A.  Jeffrey,  in  Comprehensive Supramolecular  Chemistry,      Eds.  J.  L.  Atwood,  J.E.D.  Davies,  D.D.  MacNicol,  F.  Vogtle,  J.  ? M. Lehn,  Pergamon,  Elsevier  Science,  New  York, 1996,Vol. 6, Ch.23. [2]. J. A. Ripmeester, C. I Ratcliffe, K. A. 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