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PAPER
Jonas Nyman and Graeme M. Day
Static and lattice vibrational energy differences between polymorphs
CrystEngComm
PAPER
Static and lattice vibrational energy differences
between polymorphs
Cite this: CrystEngComm, 2015, 17,
5154
contributions to polymorph free energy differences at ambient conditions are dominated by entropy
differences. The distribution of vibrational energy differences is narrower than lattice energy differences,
rarely exceeding 2 kJ mol1. However, these relatively small vibrational free energy contributions are large
enough to cause a re-ranking of polymorph stability below, or at, room temperature in 9% of the poly-
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morph pairs.
1 Introduction
Polymorphism, the possibility of a compound to exist in at
least two different crystalline phases,1 has important implications for the development of pharmaceuticals, organic semiconductors,2 explosives and any other material where solid
state properties must be controlled.3 Unexpected polymorphism can have far-reaching economic and medical,4,5 as well
as legal6 consequences. For these reasons, there is a strong
motivation to develop our fundamental understanding of
polymorphism, of property differences between polymorphs
and, ultimately, the ability to predict possible polymorphs a
priori.
The relative free energy determines which polymorph
should be favourable under given thermodynamic conditions.
However, crystallisation does not always lead to the most stable structure, with kinetic factors sometimes leading to an
alternative crystal packing. How large a lattice energy penalty
can be overcome by such kinetic factors? It is important to
understand the energy differences that can exist between
observable polymorphs. This question is particularly relevant
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2 Methods
2.1 Selection of polymorph pairs
Crystal structures were obtained from the Cambridge Structural Database (CSD), version 5.35 (Nov. 2013). Reference
code families of polymorphs in van de Streek's best hydrogens list19,20 containing only H/D, C, N, O, F, S, and Cl were
selected, the elements for which the most reliable atomatom
potentials exist. Multicomponent structures and radicals were
removed.
As our lattice dynamical treatment currently only includes
rigid molecule motions, we assume that differences in intramolecular vibrations between polymorphs are negligible. This
approximation may lead to errors when there are significant
molecular geometry differences between polymorphs, such as
in conformational polymorphism. Therefore, we used the
root-mean-square deviation (RMSD) of atomic coordinates for
molecules in different polymorphs (calculated using TORMAT,21
excluding hydrogen atom positions) to exclude structures
with large intramolecular differences. Cruz-Cabeza and Bernstein22 showed that polymorphs tend to have very similar
molecular conformations, and that an RMSD of atomic coordinates of up to 0.2250.3 usually corresponds to slight
adjustments of the same molecular conformer. We observe
essentially the same distribution as Cruz-Cabeza and Bernstein22 (see Fig. S12 in ESI) and set our limit to 0.25 , to
exclude structure pairs where molecular geometry differences
exceeded this value.
The symmetries of structures with non-integer Z were
modified to include whole molecules in the asymmetric unit.
Structures with more than 65 atoms in the asymmetric unit
were excluded to limit the computational cost of the flexible
molecule energy minimisation. Missing hydrogen atoms were
added based on conventional geometric criteria whenever
this could be done unambiguously and deuterium atoms
were substituted by hydrogen in deuterated structures. Structures with disorder or incorrectly placed hydrogen atoms
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(1)
(2)
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Z vib
i , k
exp
2kBT ,
=
i , k
i,k
1 exp
kBT
(3)
(4)
i , k
1
ln 1 exp
i , k kBT
2 i,k
i,k
kBT
(5)
The first term is the vibrational zero point energy, ZPE, while
the second term is the thermal contribution to the free
energy. The Helmholtz free energy A is obtained as
A(T) = Elatt + Fvib(T),
(6)
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i , k
S (T ) = kB ln 1 exp
i,k
kBT
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i , k
exp
1
kBT
i , k
T i,k
i , k
1 exp
kBT
(7)
2
i , k k BT
i , k
exp
1
kBT
(8)
The accuracy of calculated vibrational energy contributions depends on how well the calculations reproduce the
true vibrational frequencies, and on the sampling of reciprocal space used in calculating the partition function (eqn (3)).
Phonon calculations using the form of anisotropic atom
atom potentials employed here have previously been shown
to reproduce observed frequencies from terahertz spectroscopy with good accuracy,43,44 so that errors due to inaccuracies of the model potential should be small. The lattice
dynamics implementation in DMACRYS only provides phonons calculated at the Brillouin zone centre (k = 0). Non-zero
k-vectors were sampled by generating supercells of the original unit cell; the vibrational modes of a (N, M, P) supercell
include N M P distinct k-points of the original cell. To
ensure that our calculated energies are converged with
respect to sampling of k-points, it is important to sample as
widely as possible between k = 0 and the edge of the first
Brillouin zone. However, to obtain k-points close to 0 using
the supercell method can require very large supercells and
prohibitively long computational times. To keep computational costs manageable, we sampled k-points using combinations of linear supercells, each expanded along a single
lattice vector. Phonon frequencies from a series of supercells
are then combined. For cubic, tetragonal and orthorhombic
unit cells, the linear supercell expansion leads to k-point
sampling along the reciprocal unit cell axes a*, b*, c*. In
lower symmetry crystal systems, the sampling is not necessarily along the reciprocal lattice vectors, but should adequately
sample the dependence of phonon frequency on orientation
in reciprocal space.
In testing the convergence of calculated thermodynamic
properties with respect to k-point sampling, we set target
k-point distances along each reciprocal space direction
(length in reciprocal space per k-point). A particular target
length defined a number of k-points in that direction and,
thus, the length of the supercell. Elongated supercells were
split into several smaller supercells that sample approximately the same number of unique k-points (see ESI for a
description), providing a nearly equivalent k-point sampling
at a reduced computational cost. The individual supercells in
each direction are chosen to have mutually co-prime supercell
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RT
0Cv(T)dT TS.
(9)
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than the other at 300 K. BEBMAX has very anisotropic unit cell
dimensions and turns out to be particularly sensitive to the
phonon k-point sampling. S is still large (9.14 J mol1 K1),
but less extreme with a finer 0.08 1 sampling.
3,4-Cyclobutylfuran (XULDUD, Fig. 1c) was a target in the
first blind test of crystal structure predictions.55 It was later
discovered that XULDUD was highly unstable and a disappearing polymorph. Our calculations show that the XULDUD
structure is located at a saddle point on the potential energy
surface and symmetry breaking results in a stable Z = 2
structure. The lowering in energy is small and the observed
structure is probably a thermal average over the symmetrybroken minima. A similar phenomenon was found for only a
handful of crystal structures.
The polymorphs of 2-amino-5-nitropyrimidine (PUPBAD/
01/02, Fig. 1g), have attracted some interest before. An
attempt to calculate their relative stability and to rationalize
their polymorphic behaviour was reported by Aakery et al.56
They concluded that the orthorhombic form III (PUPBAD)
has the lowest lattice energy, but quantification of energy differences was limited by difficulties in treating molecular flexibility with their computational methods. Thermal (DSC) studies were also inconclusive. Indeed, by lattice energy, we find
that form III (PUPBAD) is much more stable than forms I
(PUPBAD01, Elatt = 6.7 kJ mol1) and II (PUPBAD02, Elatt =
7.4 kJ mol1). However, neglecting vibrational effects in these
polymorphs is misleading. The entropy differences are exceptionally large (S = 12 J mol1 K1 and 14 J mol1 K1 respectively) so that by 330 K, all three have essentially the same
free energy. This helps explain why the three polymorphs
crystallise concomitantly.56
3.6 Implications for crystal structure prediction
Fig. 8 Differences in a) lattice energy and b) entropy vs. density
differences between polymorphs. Polymorphs in each pair are ordered
such that the density difference is positive. Green and red data points
denote structures with and without hydrogen bonding. The correlation
in both cases is statistically significant to p < 109.
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crystal structure prediction studies of small organic molecules.59 The reasons why predicted polymorphs outnumber
observed polymorphs have recently been discussed by Price.60
A further observation relates to the use of lattice energy
versus free energy in predicting relative stabilities of predicted
polymorphs. Free energies should be used to assess the true
thermodynamic stabilities of structures, but are often approximated by calculated lattice energies, due in large part to the
added complexity and computational expense of free energy
calculations. However, the small magnitude of lattice energy
differences that we find between known polymorphs highlights the fact that it takes very little vibrational energy to
cause a re-ranking of polymorph stability. While a small number of studies have shown promising results from the inclusion of dynamical effects in crystal structure prediction, either
through a lattice dynamics18,6163 or molecular dynamics6466
approach, lattice energy-based predictions are still the norm.
Our results show why lattice energies have achieved good
success, particularly as the quality of lattice energy calculations has improved.14,16,67,68 The correlation between A and
Elatt is strong (R 2 = 0.85, see Fig. 9), demonstrating that lattice energy is the dominant contribution to free energy differences. However, the slope of the regression line is 0.86, not
1, reflecting our finding that Elatt and Fvib are of opposite
sign in the majority of cases; vibrational contributions in
general decrease the energy differences between polymorphs.
Furthermore, some pairs are re-ranked by the vibrational
energy, which contradicts Gavezzotti and Filippini's conclusion that free energy differences always have the same sign
as enthalpy differences.17 Differences in our conclusions may
be due to their simpler force field model, lack of intramolecular energy in their assessment of lattice energies, as well as
our different Brillouin zone sampling methods.
The green triangle in Fig. 9 marks the area where the vibrational contribution causes a discordant ranking of polymorph
Paper
4 Conclusions
Lattice energy minimisation and rigid-molecule harmonic lattice dynamics have been applied to understand thermodynamic property differences for a large set of experimentally
determined, non-disordered, packing polymorphs of organic
molecules. Our principle results are those summarised in
Fig. 3 and 4, showing the distribution of static and vibrational energy differences between polymorphs. While our
study is restricted to single-component crystal structures of
molecules containing the elements C, N, O, H, F, Cl and S,
given the large size of the structure set (1061 crystal structures in 508 polymorph families), and quality of the energy
model, we believe that these faithfully reflect true energy differences and, thus, are of great value in discussing and
understanding polymorphism.
Unsurprisingly, the lattice energy differences between
polymorphs are typically very small and are less than 7.2 kJ
mol1 in 95% of polymorph pairs. Entropies dominate the
vibrational contribution to relative free energies and, while these
contributions to relative free energies are typically small (|Fvib|
< 2 kJ mol1 in most cases), they can be large enough to significantly affect the calculated relative stability of polymorphs.
Fvib and Elatt are of opposite sign in 69% of the polymorph pairs, so that polymorph free energies usually converge with increasing temperature and will eventually cross.
By T = 300 K, we find that vibrational contributions swap the
stability order of 9% of polymorph pairs.
Correlations of energy and entropy differences with density
are weak, and there is no evidence that polymorphs of hydrogen bonding and non-hydrogen bonding molecules show different trends in thermodynamic differences. Therefore, it is
difficult to predict relative stability or thermodynamic behaviour based on these coarse descriptions of structure.
Based on the evidence presented here, computational
studies of polymorph stability, including crystal structure prediction, should not be restricted to static lattice energy calculations. The influence of lattice vibrations is important in
judging the true stability difference between polymorphs and
a necessary consideration for the anticipation of temperaturedriven phase transitions. Since the errors introduced by
restricting lattice dynamics to a single k-point are large, the
energy methods that are developed for use in the context of
crystal structure prediction should be sufficiently efficient to
allow adequate sampling of phonons without an unacceptably large computational expense. Currently, only atomatom
potentials meet these criteria and we believe that the continued development of accurate atomatom models for such
studies is necessary.
Paper
Acknowledgements
We thank Dr Manolis Vasileiadis for support and problem
solving our use of the CrystalOptimizer program. The
research leading to these results has received funding from
the European Research Council under the European Union's
Seventh Framework Programme (FP/2007-2013)/ERC Grant
Agreement no. 307358 ERC-stG-2012-ANGLE). The authors
acknowledge the use of the IRIDIS High Performance Computing Facility at the University of Southampton.
References
1 J. Haleblian and W. McCrone, J. Pharm. Sci., 1969, 58,
911929.
2 T. Siegrist, C. Besnard, S. Haas, M. Schiltz, P. Pattison, D.
Chernyshov, B. Batlogg and C. Kloc, 20792082, Adv. Mater.,
2007, 19.
3 J. Bernstein, Polymorphism in Molecular Crystals, Oxford
University Press, 2002.
4 S. R. Chemburkar, J. Bauer, K. Deming, H. Spiwek, K. Patel,
J. Morris, R. Henry, S. Spanton, W. Dziki, W. Porter, J. Quick,
P. Bauer, J. Donaubauer, B. A. Narayanan, M. Soldani, D. Riley
and K. McFarland, Org. Process Res. Dev., 2000, 4, 413417.
5 J. Bauer, S. Spanton, R. Henry, J. Quick, W. Dziki, W. Porter, J.
Quick, P. Bauer, J. Donaubauer, B. A. Narayanan, M. Soldani,
D. Riley and K. McFarland, Pharm. Res., 2001, 18, 859866.
6 W. Cabri, P. Ghetti, G. Pozzi and M. Alpegiani, Org. Process
Res. Dev., 2007, 11, 6472.
7 G. M. Day, Crystallogr. Rev., 2011, 17, 352.
8 S. L. Price, Chem. Soc. Rev., 2014, 43, 20982111.
9 J. S. Chickos and W. E. Acree, J. Phys. Chem. Ref. Data,
2002, 31, 537698.
10 L. Yu, J. Pharm. Sci., 1995, 84, 966974.
11 L. Yu, G. A. Stephenson, C. A. Mitchell, C. A. Bunnell, S. V.
Snorek, J. J. Bowyer, T. B. Borchardt, J. G. Stowell and S. R.
Byrn, J. Am. Chem. Soc., 2000, 122, 585591.
12 C.-H. Gu and D. J. W. Grant, J. Pharm. Sci., 2001, 90, 12771287.
13 J. K. Guillory and D. M. Erb, Pharm. Manuf., 1985, 2(9), 2833.
14 M. A. Neumann, F. J. Leusen and J. Kendrick, Angew. Chem.,
Int. Ed., 2008, 47, 24272430.
15 A. Otero-de-la-Roza and E. R. Johnson, J. Chem. Phys.,
2012, 137, 054103.
16 G. J. O. Beran and K. Nanda, J. Phys. Chem. Lett., 2010, 1,
34803487.
17 A. Gavezzotti and G. Filippini, J. Am. Chem. Soc., 1995, 117,
1229912305.
18 B. P. van Eijck, J. Comput. Chem., 2001, 22, 816826.
19 J. van de Streek and S. Motherwell, Acta Crystallogr., Sect. B:
Struct. Sci., 2005, 61, 504510.
20 J. van de Streek, Acta Crystallogr., Sect. B: Struct. Sci.,
2006, 62, 567579.
21 Z. F. Weng, W. S. Motherwell and J. M. Cole, J. Appl.
Crystallogr., 2008, 41, 955957.
22 A. J. Cruz-Cabeza and J. Bernstein, Chem. Rev., 2013, 114,
21702191.
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