Article

pubs.acs.org/jced

Molecular Dynamic Simulation of the Patchouli Oil Extraction

Process
F. Adam,*, Siti Hana A. B., Mashitah M. Yuso, and S. N. Tajuddin

Faculty of Chemical and Natural Resources Engineering, and Faculty of Industrial Sciences and Technology, Universiti Malaysia
Pahang, 26300 Lebuhraya Tun Razak, Gambang, Kuantan, Pahang Darul Makmur, Malaysia

ABSTRACT: Patchouli is a plant which is native in Malaysia. It is an economic crop, planted

for its essential oil. Patchouli oil has a characteristic woody scent and is used commercially as an
ingredient in fragrance and cosmetic products. The average yearly consumption around the
globe is around one metric ton. A marker compound responsible for the patchouli oil scent is
patchoulol (C15H26O). It is the major compound in patchouli oil representing around 4050%
of the essential oil composition. The aim of this study is to simulate the patchouli oil extraction
process using patchoulol as a modeled molecule in dierent solvents, namely acetone, ethanol,
and hexane. The simulation aim is to recognize molecular interaction between patchoulol
molecules with solvent molecules through hydrogen bonding and also the repulsion forces
between them due to the abundance of hydrogen atoms in the patchoulol molecule. The
simulation is equilibrated under moles, volume, and energy followed by moles, pressure, and
temperature ensembles via molecular dynamics simulation using the Material Studio software
package. The interaction in the system is analyzed through the radial distribution function to
describe the structure of patchoulol in solvent solution. The rdf trend found that the
interaction between patchoulol solutes is through the oxygen atom (O1P) and hydrogen
(H1P) atom from the hydroxyl functional group of the patchoulol molecule. In the acetone
patchoulol and hexanepatchoulol systems, the patchoulol solutes tend to self-agglomerate
indicated by rst neighboring molecules in the range of 4.25 and 5.75 , respectively, while the rst neighboring molecules of
patchoulol solutes in the binary ethanolpatchoulol system is located at 7.75 . This might suggest that the patchoulol is much
more soluble in ethanol then in acetone and hexane. The pattern observed in the simulations is in agreement with extraction
yield results obtained from the extraction experiment.

Malaysia has variety of native herb plants that produce essential
oil of which the estimated value is around RM 200 million per
year1 while the worldwide export value for essential oil in 2011
is US$ 16,483 billion.2 One of the herbs which is extracted for
essential oil is the patchouli plant or Pogostenum cablin Benth.
The patchouli essential oil has a pleasant and woody scent due
to the 24 dierent sesquiterpene3 compositions. Besides being
appreciated for the pleasant and woody scent, the patchouli oil
has various applications such as an aid in the treatment for
depression, an appetite depressant, antifungal aid, and
insecticide.47 The insecticide properties of the patchouli oil
was studied by Betty et al.,8 and it was suggested that patchouli
oil has a neurotoxic mode of action toward Formosan
Subterranean termites.
The odor of patchouli essential oil is dependent on the
composition of its marker compound. The marker compound
in the patchouli oil is the sesquiterpene patchoulol (C15H26O),
which is also the major compound at 4050% of the
composition.9 The patchoulol has been isolated from the
patchouli essential oil for use in producing an expensive
fragrance component, nor-patchoulenol.10 In addition, the
patchoulol also has been used in various studies to investigate,
in depth, a few of the patchouli properties such as the antiviral
feature. Wei and Shibamoto11 have reported that patchoulol
shows high antioxidant activity through inhibited hexanal
oxidation and 1,1-diphenyl-2-picrylhydrazyl (DPPH) scaveng-
ing assay measurement, while the most recent study by
Kiyoharaet al.12 has reported that the patchoulol showed potent
in vitro antiviral activity against inuenza virus A/PR/8/34
(H1N1). At present the patchouli plant is the only source for
the patchoulol compound because there is no developed
synthetic process to produce patchoulol for commercial
purposes.3
In recent years, the application of molecular dynamic
simulation to predict experimental theory has received interest
from chemical engineers working to understand the molecular
level interaction.13,14 Furthermore molecular simulations also
can be used to calculate properties of the individual molecules,
and they provide additional tools for observable character-
ization.15 Adam16 has applied molecular dynamics simulation to
investigate any signicant structure change in the crystallization
solution which leads to the crystallization of 2,6-dihydrox-
ybenzoic acid polymorph. The study16 found dierent
hydrogen bonding types and degrees in the polar (chloroform)
and nonpolar (toluene) solvent solutions, which lead to the
nucleation of stable and metastable crystal forms. While
Received: December 15, 2012
Accepted: December 11, 2013
Published: December 31, 2013

2013 American Chemical Society 183 dx.doi.org/10.1021/je3013292 | J. Chem. Eng. Data 2014, 59, 183188
Journal of Chemical & Engineering Data Article

Gunther et al.17 used a similar approach to predict the optimum system, the chosen atom to be referred is based on the work of
parameter to extract ()--bisabolol, aescin, harpagoside, and Kioupis et al.24 who have simulated the pure hexane system.
stachyose in pure and modied supercritical carbon dioxide
solvent. They17 suggested that solutes with heavy molecular Table 1. Simulation and Input Parameters to Represent the
weight may have a mass transfer resistance that aect the Patchouli Oil Extraction Process at 298 K and 0.0001 MPa
extraction yield. They17 also concluded that molecular dynamic (Yaws25 and Chemspider Database26)
simulation can be used to predict minimum requirement for the
densitya box size, A B C
supercritical carbon dioxide modier to extract both lipohilic
and hydrophilic compounds. no. of
system molecules g/cm3 3
This paper aims to apply the molecular dynamic simulation
technique to study the molecular interaction during the Pure System
extraction of patchouli essential oil. The commercial patchouli acetone 1000 0.793 49.556 49.556 49.556
essential oil is produced through a steam-distillation3 technique ethanol 1000 0.780 46.116 46.116 46.116
in which the high temperature may degrade the terpene hexane 1000 0.658 60.125 60.125 60.125
compounds in the oil.18 Therefore, in this study, the solvent patchoulol 50 1.000 26.421 26.421 26.421
extraction method is the main interest to be simulated. As Binary System
acetone/patchoulol 1000:20 0.804 50.537 50.537 50.537
virtual laboratory, the simulation will be able to visualize the
ethanol/patchoulol 1000:20 0.795 47.244 47.244 47.244
intermolecular interaction between solute and solvent mole-
hexane/patchoulol 1000:20 0.668 60.838 60.838 60.838
cules during the extraction process. In principle, the solvent a
that shows high interaction with the solute (patchoulol) shall Density of the mix was calculated as follows:
produce a higher extraction yield of patchouli essential oil and MWsolvent + MWsolute
higher patchoulol solubility. Three types of solvents are used in mix =
(MWsolvent/solvent ) + (MWsolute/solute )
the extraction experiment, and simulation studies include
acetone as the polar aprotic solvent, ethanol as the polar protic

solvent, and hexane as nonpolar solvent. According to
Suchoki19 and Kolar et al.20 the specic functional group
such as hydroxyl will produce specic interactions such as a
hydrogen bond that has a signicant eect on the structure of
the mixture and the solute solubility. This interaction was
believed by Pehlivanoglu et al.21 to produce a higher
distribution of polar solvent molecules which will aect the
extraction mechanism. Among the chosen solvents, ethanol has
been reported by Gironi et al.22 to be capable of reducing the
oxidizing reactions and improving the essential oil aromatics
and stability characteristics. Mostly the atoms of interest in
most of the molecules are the atoms which can contribute to
hydrogen bonding. Hydrogen bonding is classied as the
strongest intermolecular interaction.19,23 The labeled solute and
solvent molecules are shown in Figure 1, and the simulation
parameters are tabulated in Table 1. In a nonpolar hexane
Figure 1. Schematic labeling of patchoulol (a), acetone (b), ethanol
(c), and hexane (d) molecular structure.
184
METHODS
Extraction Experiment. The solvent extraction method is
used to extract the patchouli essential oil from samples which
originate from Syarikat Nilam Suling Sdn Bhd, Miri, Sarawak,
Malaysia. Acetone, ethanol, and n-hexane as the solvents were
supplied by Merck (99.7% purity). A 10 g sampling of
patchoulol leaves was soaked in 100 mL of solvent and left
overnight before undergoing the separation process using the
Buchi Evaporator (R100), and then the essential oil yield was
calculated using eq 1. The extraction experiments were
replicated three times for each solvent.
essential oil wt (g)
yield (%) = 100
sample wt (g) (1)
GCMS Analysis. The essential oils were characterized
using an Agilent 7890A Network System gas chromatography,
which was attached to a mass spectrometer (Agilent 5975C)
with detector in full scan mode under electron impact
ionization (EI, 70 eV). The GCMS is tted with a capillary
column (DB-1MS, i.d. 0.25 mm; lm thickness, 0.25 m)
with temperatures of the injector and detector set at 250 C.
Each sample was diluted in n-hexane, and 1 L of this solution
was injected in the split mode (ratio 1:20) using helium as
carrier gas (1 mL/min). The resulting mass spectra will be
compared with the internal mass spectra library to identify the
individual compounds. Conrmation of identity was done by
comparing the retention indices with those in the National
Institute of Standards Technology (NIST) library.
Simulation Details. The simulations study of the patchouli
extraction process was carried out through the molecular
dynamic simulation technique in Acceryls Materials Studio
(MS),27 version 5.5, using a HP Z400 workstation. Initially,
each of solute and solvent molecules underwent the geometry
optimization step prior to the creation of the simulation boxes.
In this study the condensed-phase optimized molecular
potentials for atomistic simulation studies28 [COMPASS]
force eld was used to model the system.
dx.doi.org/10.1021/je3013292 | J. Chem. Eng. Data 2014, 59, 183188
Journal of Chemical & Engineering Data
Sun (1998) 28 detailed the bonded and nonbonded
interaction model of the COMPASS force eld. The van der
Waals part of the nonbond interaction is modeled using the
Lennard-Jones (LJ) 9-6 function which is softer to the
repulsion region compared to LJ 12-6 function as per eq 2,
whereas eq 3 represents the Coulombic part which models the
electrostatics of the nonbond interaction.
R 9 R 6
E VDW = Do2 o 3 o
R R (2)
qiqj
ECol =
R (3)
where D is the energy parameter, R is the radius, C is the unit
conversion factor, is the relative dielectric constant, and q is
the partial charges.
The COMPASS force eld is suitable in the simulation of
organic molecules, inorganic gas molecules, and common
polymers.28 The simulation work employed the Verlet velocity
algorithm integrator with an atom-based summation method as
the cuto method for long-range interactions. The cuto used
for both van der Waals and electrostatics is 15.5 with cubic
spline truncation. The atom-based summation method is a
simple direct method to calculate the long-range nonbond
interaction, where the interaction beyond the cut o is ignored.
This cheaper calculation mode is used in this study to reduce
the simulation time period.
The simulation began with equilibration of the system under
the constant number of moles, volume, and energy (NVE)
ensemble for 100 ps. After the equilibration, the systems were
run in the NPT ensemble which is constant number of moles,
pressure, and temperature for a total simulation time of 5 ns
with 1 fs stepsize. In the NPT ensembles, the pressure of all
systems is controlled at 1 atm by coupling the system with a
Berendsen barostat with a decay constant of 0.1 ps, whereas a
Nose thermostat is used for the temperature control with a
ctitious mass, Q, ratio of 1.0. The simulation temperature is at
298 K to represent the extraction experiment which was carried
out at room temperature.
The trajectory le produced from the dynamic simulation
was analysed through calculation of the rdf which is a structural
property that can be correlated to the probability of nding the
nearest neighbor atom, gxy (r). This probability can be
described in the following expression.16,29
Ny(r , r + dr )
gxy(r ) =
y 4r 2dr ([4])
where r is the spherical radius, y is the density of the y atom,
Ny (r, r + dr) is the number of y atoms in a shell of width r at
distance r, and x is the reference atom.
RESULT AND DISCUSSION
Simulation Validation. The analyzed rdf of pure acetone,
ethanol, and hexane liquid solvent is validated and compared to
the literature data.24,30,31 The purpose of validation is to check
that the force eld is able to work well in reproducing the rdf
property in such a pure system, and therefore the force eld
should work well in the binary system. Both Figure 1 and
Figure 2 show the validation for the pure acetone and ethanol
simulation, respectively, through comparison with literature
data available. The validation for both pure acetone and ethanol
185
Article
Figure 2. Comparison of rdf for O1AO1A in pure acetone liquid
system from this study and Liang et al.30 work using the COMPASS
and OPLS force eld, respectively.
is carried out through comparison of the OO interaction
between this study with Liang et al.30 and Saiz et al.31 data,
respectively. Both graphs show the dierence in the rdf pattern.
The dierence in rdf trend might be caused by the dierent
force eld and summation method used and number of
molecules simulated.
Liang et al.30 simulated 512 acetone molecules using the
OPLS [optimized potentials for liquid simulations] force eld,
and Saiz et al.31 simulated 125 ethanol molecules up to 10 ns
with the OPLS force eld and applied the Ewald summation
method for the electrostatic interaction. The OPLS force eld is
suitable for simulation of the organic and biomolecular
systems.28 Meanwhile this study applied the COMPASS force
eld in the simulation of 1000 acetone and ethanol molecules
for 5 ns with the atom based-summation method for both van
der Waals and electrostatic interaction. Atom-based summation
requires less expensive calculations compared to the Ewald
summation in the Material Studio Package. A literature32
concluded that the atom-based summation method is an
inferior cuto method which is not suitable to calculate the
electrostatic interaction due to large errors from forces
discontinuity. In addition, a literature33 evaluation of the
Ewald summation method has concluded that if the number of
molecules N 1000, the standard Ewald summation method is
ecient to describe the electrostatic interaction in a polar
molecule such as acetone and ethanol. This would explain the
dierence of the rdf pattern in Figure 2 and the intensity of g(r)
obtained in Figure 3.
The validation of the use of the COMPASS force eld for the
pure hexane structure is shown in Figure 4. The CH3CH3
Figure 3. Comparison of O1EO1E in pure ethanol liquid system
from this study and Saiz et al.31 work using COMPASS and OPLS
force eld, respectively.
dx.doi.org/10.1021/je3013292 | J. Chem. Eng. Data 2014, 59, 183188
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Table 2. Simulation Results for Patchouli Oil Extraction

Process
average average
simulated average simulated simulated
density temperature pressure
system g/cm3 K atm
pure acetone 0.795 297.993 270.0
pure ethanol 0.804 316.0 2187.0
pure hexane 0.695 298.0 1.0
pure patchoulol 0.952 298.0 1.0
binary: acetone 0.807 297.998 214.0
patchoulol
binary: ethanol 0.801 305.4 2023.2
Figure 4. Comparison of CH3CH3 interaction in pure hexane liquid patchoulol
system from this study and Kioupis et al.24 work using COMPASS and binary: hexane 0.706 298.0 1.0
TraPPE force eld, respectively, which shows a satisfactory agreement patchoulol
in rdf.
In this work, the solutesolute interaction between O1P and
H1P atom as the reference intermolecular interaction which
represents the hydrogen bonding for pure patchoulol and
interaction of this study produced a similar pattern to the rdf solvent-patchoulol systems is the main interest for the potential
pattern in the work of Kioupis et al.,24 even with dierent total of solubility control. The rdf pattern in Figure 5 follows the
simulation time, number of molecules, and force eld used.
Kioupis et al.24 ran the molecular dynamic in the range of 25
ns with the transferable potentials for phase equilibria
(TraPPE) force eld. They simulated a range of molecules
number of hexane from 20 to 200 molecules but did not further
explain the method used to describe the long-range interaction.
The TraPPE force eld can describe the properties of linear
alkanes through the optimization of the LJ methyl and
methylene parameters.34 Similar to pure acetone and ethanol
systems, this study simulated 1000 hexane molecules using the
COMPASS force eld with the atom-based summation method
to calculate the nonbond interaction with a total simulation
time of 5 ns. The similar rdf pattern between this study and
Kioupis et al.,24 may suggest that the simulation of pure hexane
has a minimal long-range interaction eect toward the structure
produced and does not require the Ewald summation method Figure 5. The solutesolute interaction in the pure patchoulol system
to model the long-range interaction in a nonpolar system. and binary systems with O1P and H1P as reference hydrogen bond
Comparisons of validation graphs indicate that polar interaction.
molecules such as ethanol and acetone require a more accurate
summation method to reproduce an accurate rdf pattern.
Nevertheless the rdf pattern for both pure acetone and pure solid phase rdf trend because the isolated patchoulol preferably
ethanol is still reliable to describe the position of the exists as a solid crystal at room temperature.3 Therefore the
neighboring atom r, especially the ethanol rdf pattern. Kim et presence of these kind of interactions indicates a solid phase
al.35 also produced a similar rdf pattern for the carbon trend. It shows clearly that the O1PH1P interaction in binary
(polysulfon membrane)oxygen (water) interaction. ethanolpatchoulol shifted to 7.75 from 1.75 in the pure
Simulation Results. The comparison of simulated data and patchoulol system. The change reects a signicant eect to the
the setting parameters are tabulated in Table 2. Pure hexane solutesolute interaction with the presence of solvent molecule
and binary hexanepatchoulol systems have shown the highest in the binary system. The change may indicate that the
deviation from the setting value of density with 5% absolute solubility of patchoulol in the solvent occurs through the
error. However the percentage error is still in an acceptable breaking of O1PH1P hydrogen bonding. Therefore it is
range such as reported by Sun.28 His work simulated about 150 expected that ethanol will extract the highest yield of patchouli
organic structures using COMPASS force eld with a maximum oil followed by hexane and acetone from the solvent extraction
absolute error of 6% for the simulated density. The reason for experiments.
the deviation in the simulated temperature and pressure for The stronger interaction between ethanol and patchoulol
systems which contain ethanol and acetone molecules might may occur because both patchoulol and ethanol molecules have
because of the simple calculation of the atom-based summation an O atom and H atom (O1EH1P and O1PH1E) which
method. These ndings are similar in Kim et al.36 in their can establish a higher number of degree of hydrogen bond
simulation studies of benzene, toluene, and p-xylene. They have (synthons) (Figure 6), while for the hexanepatchoulol
suggested that the calculation using the atom-based summation interaction, only the London dispersion forces can be
method may not have properly addressed the polarization issue established, which are usually found between polar and
in ethanol and acetone which may aect the molecular nonpolar molecules and the London dispersion force has
movement as written by Leach.37 been classied as the weakest intermolecular force.38 Never-
186 dx.doi.org/10.1021/je3013292 | J. Chem. Eng. Data 2014, 59, 183188
Journal of Chemical & Engineering Data
Figure 6. The solventsolute intermolecular interaction in a binary
acetonepatchoulol system, ethanolpatchoulol system, and hexane
patchoulol system with O and H atom from both solvent and solute as
reference atom.
theless, this kind of interaction still plays a signicant eect on
the solutesolute interaction as revealed in Figure 5 (binary
hexanepatchoulol system). As a polar aprotic solvent, acetone
can act as a hydrogen-bond acceptor. However the repulsion
interaction of the O1AO1P presence has weakened the
O1AH1P hydrogen bonding in acetone solution. The
repulsion force presence in the binary ethanolpatchoulol
system through the O1EO1P interaction indicates less
structure and a weak interaction pattern.
To further conrm this simulation results, an experimental
work using a similar solvent type has been carried out. The
extracted essential oil is then analyzed by the GCMS to
conrm the percentage of patchoulol presence in the oil as the
key component to determine the oil quality.39 The extraction
yield and percentage area calculated by GCMS for each
sample being extracted by dierent solvents are summarized in
Table 3. Interestingly, the extraction experiment is in
Table 3. The Extraction Experiment Yield for Patchouli Oil
Extracted Using the Solvent Extraction Method
average patchouli oil average patchoulol identied by GC
yield MS
solvent wt/wt % % area
acetone 8.34 58.04
ethanol 30.99 66.17
hexane 13.15 64.55
agreement to the simulation results pattern in which ethanol
has produced the highest oil yield and acetone produced the
lowest oil yield. A stronger molecular interaction between
patchoulol and ethanol molecules has attracted more
patchoulol molecules to diuse out from the leaves matrix
into the solvent, while the lower ability of acetone to extract the
patchouli essential oil result is probably due to the presence of
O1AO1P repulsion between acetone and patchoulol
molecules. The repulsion has a signicant eect toward the
solutesolvent interaction such as seen in Figure 7. In the
hexanepatchoulol system, the interaction of O1PH3C or
London dispersion is responsible for the higher extraction of
patchouli oil compared to that in acetone. It may be concluded
that the repulsion between the abundant hydrogen atoms in
hexane and the patchoulol molecules is not as strong as the
O1AO1P repulsion in the acetonepatchoulol system.
In Table 3, GCMS has detected a high percentage of
patchoulol composition in all of patchouli oil samples. The
range indicates that the oil samples meet the market
187
Article
Figure 7. The repulsion phenomena in a binary acetonepatchoulol
system and ethanolpatchoulol system.
specication as suggested by Singh et al.39 Beside, GCMS
data also suggest that the solvent extraction method can
produce a higher quality of patchouli essential oil compared to
the hydrodistillation technique. The patchoulol compound then
can be further isolated for the production of hydroxypatchoulol,
which has similar odor to a valuable fragrance, nor-
patchoulenol.9 Besides the patchoulol compound, the analysis
detected -patchoulene, caryophyllene oxide, caryophyllene,
spathulenol, and three new unknown compounds. In this study,
both simulation work (molecular properties) and extraction
experiment (bulk properties) complement and link to each
other.
CONCLUSION
The molecular dynamic simulation approach has successfully
described the structural property of patchoulol solute in the
application of the solvent extraction process. A higher yield of
extraction in ethanol has been recognized due to the hydrogen
bonding arrangement (synthons) between the solutesolvent
molecules. The synthons is able to increase the solute solubility
in ethanol compared that in hexane and acetone. The nding is
useful for a chemical engineer to obtain insight at the molecular
scale for controlling the extraction process parameters. This
study should be further extended to understand other process
parameters such as temperature, pressure, and concentration on
the structure and synthons of the extraction process. The
molecular diusivity also should be measured to describe mass
transfer behavior during the extraction process. The Ewald
summation method is suggested to improve the model of
structural properties in the polar solvent system.
AUTHOR INFORMATION
Corresponding Author
*E-mail: fatmawati@ump.edu.my. Tel: +609-549 2824. Fax:
+609-549 2889.
Funding
The authors would like to express high appreciation for support
to Universiti Malaysia Pahang and the Ministry of Higher
Education, Malaysia, through Fundamental Research Grant
Scheme (FRGS - UMPRDU 110105).
Notes
The authors declare no competing nancial interest.
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