Structure determination of fatty acid ester biofuels via in situ cryocrystallisation and single crystal X-ray diffraction

Article abstract of DOI:10.1039/c8ce01673a

In situ cryocrystallisation in combination with a zone-melting technique enabled the crystal structure determination of a homologous series of low-melting n-alkyl methyl esters C_n-1H_2n+1CO₂CH₃, from methyl pentanoate (n = 5) to methyl tridecanoate (n = 13), by single crystal X-ray diffraction. Two isostructural groups were identified: the odd-numbered triclinic members (C_9,11,13) and the even-numbered orthorhombic members (C₈,_10,12). All observed structural trends, similarities and differences in intermolecular contacts, including the odd-even effect observable in melting point behaviour and unit cell parameters, were easily visualised and described by 2D fingerprint plots generated from the calculated Hirshfeld surfaces, in combination with atom-atom Coulomb-London-Pauli (AA-CLP) lattice energy calculations.

Full text of DOI:10.1039/c8ce01673a

Volume 21 Number 1 7 January 2019 Pages 1–192
CrystEngComm
rsc.li/crystengcomm
ISSN 1466-8033
PAPER
Cara Slabbert, Andreas Lemmerer et al.
Structure determination of fatty acid ester biofuels via in situ
cryocrystallisation and single crystal X-ray diffraction

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PAPER
Structure determination of fatty acid ester biofuels
via in situ cryocrystallisation and single crystal
X-ray diffraction†
Cite this: CrystEngComm, 2019, 21,
41
ab
Siriyara Jagannatha Prathapa,a Cara Slabbert,
*
Manuel A. Fernandes a and Andreas Lemmerer
a
*
In situ cryocrystallisation in combination with a zone-melting technique enabled the crystal structure de-
termination of a homologous series of low-melting n-alkyl methyl esters Cn−1H2n+1CO2CH3, from methyl
pentanoate (n = 5) to methyl tridecanoate (n = 13), by single crystal X-ray diffraction. Two isostructural
groups were identified: the odd-numbered triclinic members (C9,11,13) and the even-numbered orthorhom-
bic members (C8,10,12). All observed structural trends, similarities and differences in intermolecular contacts,
including the odd–even effect observable in melting point behaviour and unit cell parameters, were easily
visualised and described by 2D fingerprint plots generated from the calculated Hirshfeld surfaces, in combi-
nation with atom–atom Coulomb–London–Pauli (AA-CLP) lattice energy calculations.
Received 30th September 2018,
Accepted 5th November 2018
DOI: 10.1039/c8ce01673a
rsc.li/crystengcomm
diesels in colder climates.5 Various tactics towards tackling
these issues exist,6 including the use of additives,7–9 mixing/
Introduction
Current interest in biodiesel sprouts not only from environ-
mental concerns but also from the global shortage of fossil
fuels with the concomitant upsurge in the cost of crude oil.1
Biodiesel offers several advantages over diesel fuel, but its
widespread use is hampered by some serious economic and
technical issues related to its physical properties. Obstinate
technical problems include poor cold flow performance, de-
creased oxidative stability and increased NOx exhaust emis-
sions. Biodiesels are derived from biomass with a substantial
triglyceride content through transesterification with methanol
or ethanol in the presence of a catalyst, which leads to a mix-
ture of glycerol and fatty acid esters (FAEs). The FAE profiles
are identical to the profile of the source oil.2,3 Fuel properties,
including cold flow, are directly impacted by the structure of
composite FAEs, which makes simultaneous solving of techni-
cal issues problematic, since the resolution of one problem
may intensify the next.4 Poor cold flow properties result from
the relatively high melting points of the various FAE compo-
nents and result in the fuel solidifying at cold temperatures
to form crystalline precipitates which hampers the use of bio-
blending with mineral-derived diesel,5,10 changing the chemi-
cal structure of the FAEs by using an acyl acceptor other than
methanol/ethanol or by altering the FAE composition either
physically, by winterization,11,12 or by genetic modification of
the seed oils.6 The ignition quality of biodiesel is indicated by
the cetane number (CN)3,4 and is inversely related to the igni-
tion delay time.4 The standards for biodiesel require a mini-
mum CN of 47 (ASTM D6517) or 51 (EN14214).4 CN require-
ments therefore prevent the use particularly of fatty acid
methyl esters (FAMEs) of the general formula C4H9CO2CH3–
C12H25CO2CH3 (Scheme 1) shorter than C7H15CO2CH3 as bio-
diesel, although they have been used as surrogates in
modeling13–18 studies. Little is known about the solid state
structures and properties of the crystalline precipitates that
form at reduced temperatures. A systematic study of the
crystallisation of various pure FAMEs of biodiesel may provide
structural insights into melting point suppression with subse-
quent control by providing a solid-state chemistry model.19
Growing single crystals of the individual FAMEs, amenable
for analysis by single crystal X-ray diffraction (SCXRD), proved
challenging, since these compounds are all liquid at room
temperature (ca. 25 °C). The resurgence of SCXRD analysis of
low-melting materials, due to advances in both in situ crystal
growth techniques and equipment, is therefore timely.20 Sin-
gle crystals of the liquid FAMEs were grown by in situ
cryocrystallisation in combination with a zone-melting tech-
nique with the aid of an optical heating and cooling device
(OHCD III), as described in detail elsewhere.21–23 Hirshfeld
surface analysis24–26 and atom–atom Coulomb–London–Pauli
a Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand,
Johannesburg 2050, South Africa. E-mail: Andreas.Lemmerer@wits.ac.za;
Fax: +27 11 717 6749; Tel: +27 11 717 6711
b Department of Chemistry, University of Pretoria, Pretoria, 0002, South Africa.
E-mail: cara.slabbert@up.ac.za
† Electronic supplementary information (ESI) available: Labelled Ortep dia-
grams, packing diagrams, OHCD parameters and DSC scans. CCDC 1590402–
1590410. For ESI and crystallographic data in CIF or other electronic format see
DOI: 10.1039/c8ce01673a
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Scheme 1 The fatty acid methyl esters (FAMEs) reported in this study: C4H9CO2CH3–C12H25CO2CH3. The FAMEs were abbreviated in the text and
refer to the length of the alkyl chain, C5–C13
.
Fig. 1 General synthesis of FAMEs.
(AA-CLP)27,28 lattice energy calculations were used to enhance
the analysis of the different packing arrangements and inter-
actions present in the 3D structures. Hirshfeld surfaces allow
extraction and quantification of the contributions of different
types of intermolecular contacts to the observed crystal pack-
ing. The generated 2D fingerprint plots summarise these in-
teractions graphically, with the differences between plots giv-
ing valuable information on both non-covalent interactions
and close contacts at minimal computational costs. AA-
CLP27,28 was used to calculate lattice energies and interaction
energies of molecular pairs. This technique enables
partitioning of the total energy into electrostatic, polarization,
dispersion, and repulsion components to evaluate the impor-
tance of non-covalent interactions in the crystal packing.
methanol as both the acyl acceptor and solvent using the fol-
lowing general method: to a stirred solution of each respec-
tive carboxylic acid (0.20 g) in a large reagent excess of meth-
anol (15 mL), a catalytic amount of H2SO4 (conc., 5.0 mol%)
was added at room temperature (ca. 25 °C). The solution was
heated at reflux for approximately 3 h, with the reaction prog-
ress monitored by thin layer chromatography (TLC). After
completion, the reaction vessel was left to cool to room tem-
perature, whereafter the solution was diluted with hexane (15
mL). The layers were separated and the aqueous layer
extracted with hexane (3 × 20 mL). The combined organic
layers were washed with NaHCO3 (sat. aq., 2 × 10 mL) and
brine (2 × 20 mL), dried (NaSO4), filtered and evaporated un-
der reduced pressure, with the bath temperature dictated by
the volatility of the expected ester product, to yield the prod-
ucts as colourless liquids. No further purification was neces-
sary. Yields ranged from 60% to near quantitative.
Experimental
Synthesis
In this work, a continuous range, starting from C4H9CO2CH3–
C12H25CO2CH3, of FAMEs were synthesised (Fig. 1), following
a standard Fischer esterification procedure,29 from the re-
spective even- and odd-numbered neat carboxylic acid with
Single crystal X-ray diffraction studies
Single crystals of the liquid FAMEs were grown via in situ crys-
tallization in a 0.3 mm diameter Lindemann capillary using
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Fig. 2 The general view of an individual mono layer in C5 (a), which
can be described by how the molecules arrange within the layer in two
crystallographic directions. The third descriptor is then how individual
mono layers arrange relative to each other (b).
the OHCD. Diffraction quality crystals were grown using a
zone-melting technique where a small region of the capillary
was heated with a CO2 IR laser to create a molten zone (the
temperature of which is sample dependent and slightly below
the melting temperature of the pure sample). Melting points
were recorded and the DSC traces for all compounds are given
in the ESI.† The molten zone was slowly moved along the
length of the capillary at about 3 cm/30 min by adjusting the
position of the laser and allowing for recrystallization of the
molten zone.22,23 The cycle was repeated several times until a
single crystal amenable for analysis by SCXRD was obtained.
The number of cycles, cycle time and laser intensity required
to obtain a good quality single crystal is sample dependent,
and the whole process can take several days (further details
are provided in the ESI†). Since the samples are sensitive to
temperature and melt easily, the whole experiment was carried
out in the measurement device (the diffractometer), hence the
term in situ. In general, the crystal size of C5–C13 was esti-
mated to be 1.00 mm × 0.30 mm × 0.30 mm. Single crystal
data of the liquid FAMEs were collected on a BRUKER D8 VEN-
TURE X-ray diffractometer equipped with a Photon 100 CMOS
camera using Mo-Kα (0.71073 Å) radiation. The crystal-to-
detector distance was fixed at 80 mm for all the crystals to
maintain uniformity over data collection. Complete data sets
were collected for all the compounds by the strategies gener-
ated using the APEX3 module of the Bruker software suite.
The scan width per frame was Δω = 0.5°. The cell refinement
and data reduction were carried out using SAINT+30 and multi-
scan absorption correction was performed using the program
SADABS.31 The crystal structures were solved by SHELXTL32,33
structure solution software and were refined with full-matrix
least squares on F2 included in the WinGX package suite.34
Non-hydrogen atoms were refined anisotropically and hydro-
Fig. 3 Views of the monolayers of C5–7. Note that the monolayers of
these early members of the series do not show any consistency,
packing head-to tail in both directions in C5 (a), head-to-head and tail-
to-tail in C6 (b) and head-to-head and head-to-tail in C7 (c).
gen atoms were fixed on geometrically ideal positions during
the refinement. Twin laws were required in the refinements of
C5, C6, C9, C11 and C13. The atomic numbering scheme and
ORTEP style displacement ellipsoids for all the structures are
given in the ESI.†
Hirshfeld surface calculations
Molecular Hirshfeld surface calculations were performed
using the CrystalExplorer-3.1 (ref. 35) program. The bond
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Table 2 Hydrogen bonding geometries involved in FAMEs C5–13
FAMEs
D–H⋯A
D–H (Å)
H⋯A (Å)
D⋯A (Å)
D–H⋯A (°)
Symmetry
C5
C6
C(2)–HIJ2A)⋯OIJ1)
C(2)–HIJ2B)⋯OIJ2)
C(4)–HIJ4A)⋯OIJ2)
C(8)–HIJ8A)⋯OIJ2)
C(8)–HIJ8B)⋯OIJ2)
C(2)–HIJ2A)⋯OIJ2)
C(3)–HIJ3A)⋯OIJ2)
C(2)–HIJ2B)⋯OIJ4)
C(12)–HIJ12B)⋯OIJ4)
C(20)–HIJ20A)⋯OIJ2)
C(2)–HIJ2B)⋯OIJ2)
C(3)–HIJ3B)⋯OIJ2)
C(2)–HIJ2A)⋯OIJ4)
C(14)–HIJ14A)⋯OIJ4)
C(24)–HIJ24A)⋯OIJ2)
C(2)–HIJ2B)⋯OIJ2)
C(3)–HIJ3A) ⋯OIJ2)
C(2)–HIJ2B)⋯OIJ4)
C(16)–HIJ16B)⋯OIJ4)
C(28)–HIJ28B)⋯OIJ2)
0.99
0.99
0.99
0.98
0.98
0.99
0.99
0.99
0.99
0.98
0.99
0.99
0.99
0.99
0.98
0.99
0.99
0.99
0.99
0.98
2.69
2.52
2.71
2.62
2.70
2.63
2.63
2.50
2.71
2.62
2.61
2.63
2.53
2.70
2.63
2.61
2.63
2.54
2.69
2.61
3.670(7)
3.448(6)
3.587(6)
3.416(2)
3.573(2)
3.542(5)
3.393(5)
3.225(5)
3.612(5)
3.569(5)
3.527(7)
3.398(6)
3.254(3)
3.606(3)
3.583(3)
3.529(4)
3.408(5)
3.248(7)
3.600(7)
3.582(7)
169
156
148
138
149
154
134
130
152
163
154
135
130
152
166
155
135
129
152
170
−x + 1, −y + 1, −z + 1
x, −y + 1, z + 1/2
x, −y + 1, z + 1/2
x, y − 1, z
C7
C8
C9
−x + 1/2, y − 1/2, −z + 3/2
x, y, z – 1
x, −y + 1, z − 1/2
x + 1, y, z
−x + 1, −y + 1, −z + 1
C10
C11
x, y, z – 1
x, −y, z − 1/2
x + 1, y, z
−x, −y + 1, −z + 1
C12
C13
x, y, z + 1
x, −y + 1, z + 1/2
x + 1, y, z
−x, −y + 1, −z + 1
Table 3 Relevant distances (Å) and angles (°) within layer arrangements for compounds C5–7
Head-to-head
Tail-to-tail
Head-to-tail
O–CH3⋯CH3–O (Å)
C–CH3⋯H3C–C (Å)
O–CH3⋯H3C–C (Å)
C5
C6
C(6)⋯OIJ2)i: 3.843(8)
—
—
—
—
C(7)⋯C(7)ii: 3.377(7)
(i): 1/2 − x, 1/2 − y, −z; (ii): 1/2 − x, 3/2 − y, −z.
lengths to hydrogen were automatically modified to the stan-
dard neutron values (C–H = 1.083 Å) upon using the respec-
tive cif-files as input. The 2D fingerprint plots, with de and di
distance scales displayed on the respective graph axes, were
generated using the standard 0.6–2.6 Å view.
perature and energy calibrations were performed using pure in-
dium (purity 99.99%, m.p. 156.6 °C, heat of fusion 28.45 J g−1).
Results and discussion
Reported here are the crystal structures of the compounds
(C4H9CO2CH3–C12H25CO2CH3) which are all liquid at room
temperature and in which crystallisation was achieved by in
situ cryocrystallisation. All compounds had an all-trans con-
formation. For simplicity, we will refer to the FAMEs as Cn,
where n is the number of fatty acid carbons, e.g. C4H9CO2CH3
is abbreviated to C5. All crystallographic parameters are given
in Table 1. The discussion is structured according to space
group assignment, with the monoclinic C5,6,7 triad discussed
in isolation, since, as also noted by Bond,36 “the early mem-
bers of most homologous chemical series display substantial
deviation in their crystal structures”. From C8 onwards, the
unit cell dimensions resemble those of some membrane
lipids,37 as well as those of the orthogonally derived unit cells
AA-CLP calculations
Lattice and molecule⋯molecule interaction energies were
calculated using the August 2014 version of AA-CLP.27 Atom
coordinates for all calculations were taken from X-ray diffrac-
tion studies with normalization of H-bond positions as
implemented in the CLP computer program package. The
fully empirical atom–atom Coulomb–London–Pauli (AA-CLP)
force field model was applied with default scaling parameters
for coulombic, polarization, dispersion and repulsion terms
for quick estimation of approximate lattice energies.
Differential scanning calorimetry (DSC)
of the homologous series of n-alkyl carboxylic acids (C6–15
)
Differential scanning calorimetry data (Table S2†) were col-
lected using a Mettler Toledo 822e with aluminium pans un-
der air purge. Star SW 9.20 was used for instrument control
and data analysis. Exothermic events were shown as peaks.
Various heating and cooling protocols were performed to deter-
mine temperatures and enthalpies of phase changes. The tem-
reported by Bond.36 In this work, two isostructural groups
were identified: the even-membered orthorhombic members
(C8,10,12) and the odd-membered triclinic members (C9,11,13).
As suggested by Bond,36 on the crystal structures of a homol-
ogous series of n-alkyl carboxylic acids, the discussion of the
crystal structures can conveniently be separated into packing
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adjacent molecules, we will refer to the hydrophilic ester part
as the head section and the hydrophobic alkyl part as the tail
section. Any weak hydrogen bonds and short contacts were
identified using the default settings in MERCURY.41
Structural commentary on C5–7
The C5–7 n-alkyl esters crystallise in monoclinic space groups,
each with Z′ = 1. The C5 and C7 FAMEs crystallize in primitive
space groups and C6 in C-centered. In structure C5, the mono-
layer in the bc-plane overall resembles a chevron arrangement,
with adjacent molecules packing head-to-tail (parallel) along the
c-axis and head-to-tail (anti-parallel) along the b-axis (Fig. 3a).
There exists a short contact between the carbonyl OIJ2)C and
methyl C(6) within this monolayer (Fig. 4a and Table 3). Adja-
cent monolayers are stabilised by two symmetry equivalent
C(2)–HIJ2A)⋯OIJ1)–C hydrogen bonds forming an R22(8) hydro-
gen bonded ring (Fig. 4a). In contrast, in C6, the molecules
within monolayers defined by the ac-plane pack head-to-tail
(parallel) in both the a-axis and c-axis (Fig. 3b). Adjacent mole-
cules in this monolayer interact via two C(4)–HIJ4A)⋯OIJ2)C
and C(2)–HIJ2B)⋯OIJ2)C hydrogen bonds forming an R12(6)
ring and a short contact exists between the methyl groups, C(7),
of the head section (Fig. 4b and Table 3). This forms a lamellar
arrangement. C7, being odd-membered, shows the same chev-
ron arrangement as C5 where adjacent molecules pack head-to-
head (parallel) along the b-axis but head-to-tail (anti-parallel)
along the (101) direction (Fig. 3c). Adjacent monolayers interact
via C(8)–HIJ8A)⋯OIJ2)C and C(8)–HIJ8B)⋯OIJ2)C hydrogen
bonds to form repeating R23(9) rings (Fig. 4c).
Packing and hydrogen bonding description for C8,10,12
The even-membered C8,10,12 all crystallise in the orthorhom-
bic space group Pbcn with Z' = 1 and are isostructural. Again,
starting to describe the arrangement of molecules within a
monolayer makes for an easier comparative description. In
all the structures, the monolayer is defined by the ac-plane.
Adjacent molecules pack head-to-head (parallel) along the
c-axis, and alternatingly head-to-head (parallel) and tail-to-tail
(anti-parallel) along the a-axis (Fig. 5a). This results in an
overall herringbone arrangement in C6 (Fig. 5a), unlike the
chevron arrangement in C5 and C7. At the interface of the
head groups, the molecules are braided together via weak
C(2)–HIJ2A)⋯OIJ2)C hydrogen bonds along the a-axis
(Fig. 6a). Molecules in adjacent layers interact via a C(3)–
HIJ3A)⋯OIJ2)C hydrogen bonds along the b-axis (Fig. 7a).
The same description of the packing and hydrogen bonding
for C10 and C12 holds as for C8 (shown in Fig. 5b and c).
The distance between aligned head methyl groups in-
crease slightly through C8,10,12, with the dihedral angle be-
tween linearly aligned carbonyl functionalities at ca. 131–
133° (Table 4). The terminal carbon atoms of the tail end
methyl groups are equidistant within the respective layers,
with the C⋯C distances decreasing through C8,10,12. The an-
gle formed between flanking terminal carbon atoms
Fig. 4 Hydrogen bonding views showing the weak C–H⋯OC and
C–H⋯O–C hydrogen bonds in C5–7 (a–c). Note the short contact of the
head groups of C5 and C6. For detailed geometrical parameters see
Tables 2 and 3.
arrangement
descriptions
‘within
layers’, ‘between
layers’.38–40 A representative example of this ‘layer’ descrip-
tion for C5 is shown in Fig. 2, showing the packing arrange-
ment of the molecules shown in red within an individual
monolayer (Fig. 2a), and the relative packing between two
monolayers (red and blue coloured molecules), shown side-
on (Fig. 2b). When describing the relative arrangements of
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Fig. 5 The most marked difference is that the even-membered FAMEs have a herringbone arrangement (a–c) and the odd-membered have a
lamellar arrangement (d–f).
increases towards 90°, through C8,10,12 (Table 4), and results
in a herringbone packing arrangement at this interface
(Fig. 5). Molecules in adjacent layers (between layers) are
tilted relative to each other with the tilt angle increasing
down the series (Table 4). The weak C(3)–HIJ3A)⋯OIJ2)C hy-
drogen bonding and dispersive interactions responsible for
cohesion between layers in the b-direction (Fig. 7a) also cor-
respond to the largest contributory term Ed (e.g. C8: −91.8 kJ
mol−1) of the total calculated lattice energies, Et (e.g. C8:
−96.3 kJ mol−1), as calculated using the atom–atom approach
of the CLP27,42 manifold as collated in Table 5. The terminal
methyl groups at the tail ends of the chains line up between
adjacent layers, to form a linear interface between adjacent
layer stacks.
membered ones) and tail-to-tail (parallel; anti-parallel in the
even-membered) along the c-axis (Fig. 5d–f). This no longer
results in an overall herringbone arrangement as seen in the
even-membered C8,10,12 but more akin to the lamellar ar-
rangement seen for C6 (Fig. 3b). The hydrogen bonding be-
tween the head groups of mol1 and mol2 aligned along the
c-axis consists of C(20)–HIJ20A)⋯OIJ2)C hydrogen bonds.
However, and this is the reason for the non-equivalence of
mol1 and mol2, mol2 has a C(12)–HIJ12B)⋯OIJ4)C hydrogen
bond using the carbonyl CO acceptor. In mol1, no such hy-
drogen bond is formed. Cohesion between layers is afforded
by a weak C(2)–HIJ2B)⋯OIJ4)C hydrogen bond, as well as
short CO⋯CO contacts and dispersive interaction be-
tween the alkyl chains (Fig. 7b). As was the case in the even
C8,10,12, the molecules in adjacent layers are tilted relative to
each other in the b-direction, with the angles between the rel-
evant molecular planes larger than those observed for C8,10,12
and increasing down the series (Table 4). The methyl groups
at the tail ends of the molecules, within layers, form a ser-
rated interface between adjacent layer stacks, showing partial
interdigitation of the chain ends of the molecules at the layer
interface. In this case, the tail-ends of adjacent layers are ar-
ranged in a lamellar fashion (Fig. 4), with the distances be-
tween the terminal methyl groups slightly shorter than those
of the even-membered members but also decreasing slightly
from C9–13 (Table 4).
Packing and hydrogen bonding description for C9,11,13
The odd-membered C9,11,13 all crystallise in the triclinic space
¯
group P1 with Z' = 2 and are isostructural. The two molecules
in the asymmetric unit are labelled mol1 (ester groups O(1) &
O(2)) and mol2 (ester groups O(3) & O(4)). By inspecting the
cell angles, all being close to 90°, a higher symmetry crystal
system and space group would be expected with Z' = 1. How-
ever, the two molecules in the asymmetric unit have different
hydrogen bonding interactions and show distinct fingerprint
plots, which will be discussed further below. Nonetheless, in
C9, the monolayer is again defined by the ac-plane, with a dif-
ference arising in the alignment along one of the axis direc-
tions. Adjacent molecules pack head-to-head (parallel, identi-
cal to the even-membered ones) along the a-axis, and
alternatingly head-to-head (parallel, identical to the even-
Comparative structural commentary on C8–13
In compounds C8–13, when considering the unit cell lengths,
the shortest axis at ca. 5.5 Å corresponds to the distance
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Fig. 6 Detailed views of the hydrogen bonding arrangements of C8–13 (a–f). For detailed geometrical parameters see Tables 2 and 4.
between laterally adjacent molecules within the respective
layers. The b-axis unit cell lengths alternate between odd-
and even-membered members of the series, with the even
members displaying the shorter distances but increasing
overall across the series from C8–13. This distance, at ca. 7.1 Å
for C8,10,12 and at ca. 7.2 Å for C9,11,13, corresponds to double
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Fig. 7 Representative arrangements of two mono layers for the even-membered (a) and odd-membered (b) C8–13 FAME series. For detailed geo-
metrical parameters see Table 2.
Table 4 Relevant distances (Å) and angles (°) within layer arrangements for compounds C8–13
Head-to-head
Dihedral angle between carbonyl
Tail-to-tail
O–CH3⋯CH3–O (Å)
roups at ester interface (°)
C–CH3⋯H3C–C (Å)
Even-chain
C8
C10
C12
Odd-chain
C9
C11
C(9)⋯C(9)i: 3.370(7)
C(11)⋯C(11)iii: 3.366(9)
C(13)⋯C(13)v: 3.406(7)
132.6(3)
131.1(4)
131.8(3)
C(8)⋯C(8)ii: 4.019(6)
C(10)⋯C(10)iv: 3.982(8)
C(12)⋯C(12)vi: 3.971(6)
C(10)⋯C(20)vii: 3.507(6)
C(12)⋯C(24)ix: 3.497(4)
C(14)⋯C(28)ix: 3.512(8)
57.1(4)
57.1(2)
56.0(5)
C(9)⋯C(19)viii: 3.941(6)
C(11)⋯C(23)viii: 3.927(4)
C(13)⋯C(27)x: 4.00(1)
C13
(i): 1 − x, y, 5/2 − z; (ii): 3/2 − x, 1/2 − y, −1/2 + z; (iii): −x, y, 5/2 − z; (iv): 1/2 − x, 1/2 − y, 1/2 + z; (v): 1 − x, y, −1/2 − z; (vi): 1/2 − x, 3/2 − y, z + 1/2;
(vii): −x, 1 − y, 1 − z; (viii): 3 − x, 1 − y, −z; (ix): −1 − x, 1 − y, 1 − z; (x): x, 1 + y, z.
the distance between the defined layers. The observed oscilla-
tion in the b-axis unit cell length coincides with a decreased,
alternating accordingly, relative contribution of the close
O⋯H, C⋯O and O⋯O intermolecular contacts to the 2D fin-
gerprint plots (Fig. 9), generated from the calculated
Hirshfeld surface areas, with the O⋯O intermolecular con-
tacts only present in the odd C9,11,13 members of the series
(Table 6).25,26 The observed alternation in the b-axis unit cell
length also reflects in the calculated AA-CLP coulombic en-
ergy (Ec) term which shows the same alternation when con-
sidering the total lattice energies calculated for each com-
pound (the sequence from C8–13 is as follows: Ec = −8.5, −8.1,
−8.3, −8.0, −8.3 and −8.8 kJ mol−1). This may result from the
tilt angle between the molecular planes, with concomitant
positioning of the ester functionalities and resulting weak hy-
drogen bonding interactions along this direction. This exact
yet opposite trend was observed by Boese et al.23 upon con-
sidering a homologous series of short-chain n-alkanes and
was attributed as a compensating consequence of the pro-
nounced differences observed in the long axes. In the case of
our FAMEs, the long axes increase overall across the series
but alternate between the odd- and even-membered members
of the series. This trend has also been rationalised by Bond36
upon his investigation of a homologous series of n-alkyl car-
boxylic acids. In the case of our FAMEs, however, the exact
opposite is observed in that doubling of the long axes is ob-
served in the even-membered members of the series, from
C8–13. This may be due to the herringbone packing arrange-
ment adopted by the even-membered members compared to
the lamellar arrangement adopted by odd members. As is
common for most terminally substituted n-alkane deriva-
tives,36 the n-alkyl methyl esters considered in this paper also
present melting point alternations34 between the odd- and
even-membered compounds comprising this series. This is
depicted graphically in Fig. 8 for C8–13 showing the systemati-
cally lower melting point of the odd members C9,11,13 (see
Table 6).
Table 5 Results of AA-CLP calculations as partitioned lattice energy con-
a
tributions (kJ mol−1
)
to the total calculated lattice energies of the C5 to
C13 FAMEs
Ec
Ep
Ed
Er
Et
C5
C6
C7
C8
−9.8
−8.8
−10.5
−8.5
−8.1
−8.3
−8
−27.6
−31
−69
32.4
23.9
42.2
39.8
32.3
34.5
35
−74.1
Hirshfeld and fingerprint plot analysis for C8–13
−69.9
−90
−85.9
The 2D fingerprint plots (Fig. 9) generated from the calcu-
lated Hirshfeld surfaces give a visual depiction of the inter-
molecular interactions with concomitant trends, reaffirming
the value of the Hirshfeld surface as a valuable tool for the
speedy comparison and analysis of molecular structures.25,26
In Fig. 8, these plots are arranged into two main columns,
which separates the even-numbered (left) and odd-membered
(right) C8–13 FAME series. Each main column is further
−33.6
−35
−91.9
−91.8
−95.4
−104.1
−109.9
−128.8
−138.2
−96.3
C9
−38.4
−41.6
−43.3
−45.2
−47.8
−109.5
−119.6
−126.2
−130.8
−139.2
C10
C11
C12
C13
−8.3
−8.8
51.5
55.5
a
Total lattice energies (Et), coulombic energies (Ec), polarization
energies (Ep), dispersion energies (Ed), and repulsion (Er) terms.
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Fig. 8 Fingerprint plots for the even- (left) and odd-membered (right) FAMEs, resolved into H⋯H and H⋯O contacts, with the full fingerprint plot
displayed as a grey shadow beneath each decomposed plot. Note the difference between mol1 and mol2 for the odd-membered C9,11,13 plots.
Fig. 9 Line chart depicting the melting points (T/°C) of the C8–13 FAMEs.
resolved to highlight the O⋯H and H⋯H contacts for each
compound (includes reciprocal contacts). Immediately evi-
dent from these plots is the soft pointy shape of the
decomposed O⋯H plots. In these O⋯H fingerprint plots, the
spikes correspond to weak CH2⋯OC hydrogen bond inter-
actions in C8,10,12 and CH3⋯OC and CH2⋯OC interac-
tions in C9,11,13. The top left spikes, where di < de, corre-
spond to surface points around the –CH2/–CH3 donor
surfaces, while the bottom right counter spikes (de < di) re-
semble the surface around the OC acceptor surfaces. The
O⋯H plots of the even-membered all show additional sec-
ondary wings which portray long distance CH2⋯OC inter-
actions, which are absent in the odd members due to the dif-
ferent orientation of the carbonyl groups relative to each
other between molecules in the b-direction as well the lateral
slippage present between odd-numbered molecules in the
same direction. The analogous O⋯H plots of C9,11,13 show a
substantial number of points at large de and di, which are ab-
sent in the plots of their even-numbered counterparts, and
depict long range CH3⋯O–CH3 interactions caused by the lat-
eral slippage mentioned above. The light blue stripes accen-
tuating the O⋯H wings in the plots of the even members
50 | CrystEngComm, 2019, 21, 41–52
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Table 6 The melting points and relative percentage contributions (out of 100%) to the 2D fingerprint plots generated from the calculated Hirshfeld sur-
faces for the close H⋯H, O⋯H, C⋯H, C⋯O and O⋯O intermolecular contacts in C5–13
FAMEa
m.p.b (°C)
H⋯H (%)
H⋯O (%)
C⋯H (%)
C⋯O (%)
O⋯O (%)
C5
C6
C7
C8
−90.7
−69.6
−55.8
−36.7
−34.4
−12.8
−11.4
4.9
71.5
77.1
77.2
79.9
83.4/80.9
82.9
85.7/83.3
85.1
25.4
19.9
20.2
18.1
14.0/16.5
15.4
12.0/14.4
13.4
3.1
0.6
2.5
1.3
1.0/1.0
1.1
0.9/0.9
0.9
0.0
1.0
0.0
0.7
0.9/0.9
0.6
0.8/0.8
0.6
0.0
1.3
0.2
0.0
0.7/0.8
0.0
0.6/0.7
0.0
C9
C10
C11
C12
C13
5.9
87.4/85.4
10.6/12.6
0.7/0.7
0.7/0.7
0.6/0.6
a
b
For compounds with Z' = 2, the values were calculated for each molecule (mol1/mol2 respectively) in the asymmetric unit. Ref. 43.
show that a larger fraction of points on the calculated
Hirshfeld surfaces of the C8,10,12 FAMEs include O⋯H inter-
actions as compared to the duller colour observed in the odd-
numbered plots. The intensity of the light blue highlights de-
creases from C8 to C13, mirroring the decreasing contribution
of the AA-CLP coulombic energies Ec to the total calculated
lattice energies and in which the Ec contribution is systemati-
cally smaller for the odd members, as described above.
The decomposed plots depicting the reciprocal H⋯H
interaction of the C8–13 FAMEs resemble the 2D fingerprint
plots of the n-alkanes reported by Spackman and
McKinnon.25 The red highlighted area present in the H⋯H
plots of C8,10,12 indicates that a large fraction of points on
the Hirshfeld surfaces involve closely aligned H⋯H contacts
between the n-alkyl chains as well as at the two methyl group
interfaces at the tail part of the molecules. The said dab is
lighter in the plots of C9,11,13 although the colour intensifies
with the increase in hydrocarbon chain length. The red dab
grows in size down the series, indicating the increase in
length of the alkyl chain and the concomitant increase in dis-
persive interactions (Ed = −91.8; −104.1, −128.8 for C8,10,12; Ed
= −95.4; −109.9; and 138.2 kJ mol−1 C9,11,13).
ac-plane, the molecules arrange into layers, braided together
at the head group ends via weak hydrogen O–(CH3)⋯O–(CH3)
bonds in a linear head-to-head fashion. The distance between
aligned head methyl groups increases slightly from C8 to C13.
The angle formed between flanking terminal carbon atoms
results in a herringbone packing arrangement at this inter-
face, while the lateral packing mode is rectangular. In the odd-
membered triclinic counterparts, when viewed within layers,
the molecules arrange in a head-to-head lamellar fashion via
weak O–(CH3)⋯OC hydrogen bonds. The tail-ends of adja-
cent molecules also arrange in a lamellar fashion in this triad.
All observed structural trends, including the odd–even effect ob-
servable in the oscillating nature of the melting points and unit
cell parameters along the series, are easily visualized and de-
scribed by 2D fingerprint plots, generated from the calculated
Hirshfeld surfaces, in combination with AA-CLP lattice energy
calculations, performed using the CLP program package.
Conflicts of interest
There are no conflicts to declare.
Conclusions
Acknowledgements
The crystal structures of a continuous range of FAMEs
(C4H9CO2CH3–C12H25CO2CH3) were elucidated from SCXRD
data. The single crystals of these compounds, which are liq-
uid at room temperature, were successfully grown via in situ
cryocrystallisation in combination with a zone-melting tech-
nique. The early members of the series, C5–7, crystallised in
monoclinic space groups, while the structures of C8–C13 ar-
ranged themselves into two isostructural groups: the odd-
membered triclinic (C9,11,13) and the even-membered ortho-
rhombic (C8,10,12). In the C5–C7 n-alkyl ester triad, the mole-
cules comprising structures C5 and C6 are woven together via
The authors wish to acknowledge the Claude Leon Founda-
tion and NRF Green Economy Fund (Grant UID: 98053) for fi-
nancial assistance. They would also like to acknowledge the
NRF (Grant UID: 78572) for the purchase of the D8 VENTURE
and OHCD device. This article is dedicated to Professor Ro-
land Boese for his development of in situ cryocrystallography.
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