MOLECULAR INTERACTION OF PATCHOULI EXTRACTION PROCESS

USING MOLECULAR DYNAMIC SIMULATION APPROACH

SITI HANA BINTI ABU BAKAR

Thesis submitted in fulfilment of the requirements

for the award of the degree of

Master of Engineering (by research) in Chemical Engineering

1.

2.

3.

4. Faculty of Chemical and Natural Resources Engineering

UNIVERSITI MALAYSIA PAHANG

JULY 2014

vii

ABSTRACT

Patchouli is one of the native commercial crops in Malaysia which has various

applications in the fragrances and cosmetics industries as well as in alternative medicine

area. These are due to the interesting pharmacological properties and aroma of its

essential oil. Currently, patchoulol, a marker compound is still not produced

synthetically. The demand for patchouli essential oil will increase as patchoulol has

been found to possess antiviral property specifically towards H1N1 virus. This study

aims to recognise the intermolecular interaction during the patchouli extraction process

through the application of molecular dynamics simulation and explaining the process at

molecular scale with the extraction yield as a correlation. Therefore this study is

focussed on the solvent extraction experiment and molecular dynamic simulation.

Simulation works comprise comparison between hydro-distillation and solvent

extraction techniques with three types of solvents; the polar protic, polar aprotic and

non-polar solvents. The temperature variation effect on solvent extraction is also

simulated. Results suggest that a polar protic solvent of ethanol can establish a higher

degree of hydrogen bonding and produce the highest extraction yield (30.99% wt/wt)

which suggested a good correlation. Meanwhile an interesting finding is that hexane as

non-polar solvent managed to shift the O1P---H1P interaction up to 5.75Å from 1.75Å

in pure patchoulol system and extracted patchouli oil in higher yields compared to polar

aprotic solvent of acetone. The molecular dynamics simulation work revealed that there

is repulsion between O1A---O1P atom which may retard the solute solubility and

produced the lowest extraction yield. The molecular dynamics simulation enable

visualisation of the hydrophobic character of the patchoulol compared to well distribute

solute in the ethanol solvent extraction binary system. The temperature variation effect

study found that the small temperature increment of 5K may be the reason for a slight

perturbation in the interaction structure which was captured by the molecular dynamics

simulation.

viii

ABSTRAK

Nilam adalah salah satu tanaman komersial asli di Malaysia yang mempunyai pelbagai

aplikasi dalam industri wangian dan kosmetik serta sebagai perubatan alternatif. Ini

adalah disebabkan oleh sifat-sifat farmakologi yang menarik dan aroma minyak patinya.

Pada masa ini patchoulol sebagai sebatian penanda masih tidak boleh dihasilkan secara

sintetik. Permintaan untuk minyak pati nilam dijangka akan meningkat disebabkan

penemuan sifat farmakologi menarik patchoulol sebagai anti virus terutamanya terhadap

virus H1N1. Kajian ini bertujuan untuk mengenal pasti interaksi molekul semasa proses

pengekstrakan nilam menerusi penggunaan simulasi dinamik molekul dan digunakan

untuk menjelaskan proses pada skala molekul dengan hasil pengeluaran sebagai petanda

korelasi antara dua perkara ini. Terdapat dua aktiviti utama dalam kajian ini iaitu

eksperimen pengekstrakan pelarut dan kerja-kerja simulasi. Kerja-kerja simulasi terdiri

daripada perbandingan antara teknik penyulingan hidrodan teknik pengekstrakan

menggunakan pelarut dengan tiga jenis pelarut iaitu pelarut kutub protik, kutub aprotik

dan bukan polar. Kesan perubahan suhu pada pengekstrakan pelarut juga turut

disimulasi. Keputusan simulasi menunjukkan bahawa pelarut etanol sebagai pelarut

polar protik boleh menghasilkan ikatan hidrogen yang lebih banyak serta kadar

pengeluaran ekstraksi yang tinggi (30% berat/berat) yang menunjukkan pertalian yang

baik antara kerja simulasi dan eksperimen pengekstrakan. Sementara itu satu penemuan

menarik ialah heksana sebagai pelarut bukan kutub berjaya menjarakkan interaksi O1P-

--H1P sehingga 5.75Å daripada 1.75Å dalam sistem patchoulol tulen dan mengekstrak

minyak nilam yang lebih tinggi berbanding dengan pelarut kutub aprotik, seperti aseton.

Simulasi molekul dinamik menunjukkan bahawa terdapat penolakan O1A---O1P atom

yang mungkin mengurangkan keterlarutan bahan larut dan menghasilkan hasil

pengeluaran yang rendah. Simulasi molekul dinamik dapat menggambarkan sifat

hidrofobik bahan larut patchoulol berbanding dengan penyerakkan bahan larut yang

baik di dalam sistem binari pelarut etanol-patchoulol bagi teknik ektraksi menggunakan

pelarut. Kajian kesan perubahan suhu mendapati bahawa kenaikan suhu yang kecil iaitu

hanya 5K menghasilkan perubahan yang kecil didalam struktur interaksi, namun masih

dapat diukur oleh simulasi molekul dinamik.

ix

TABLE OF CONTENTS

Page

SUPERVISOR’S DECLARATION iii

STUDENT’S DECLARATION iv

DEDICATION v

ACKNOWLEDGEMENT vi

ABSTRACT vii

ABSTRAK viii

TABLE OF CONTENTS ix

LIST OF TABLES xii

LIST OF FIGURES xiii

LIST OF SYMBOLS xvii

LIST OF ABBREVIATIONS xix

CHAPTER 1 INTRODUCTION

1.0 Introduction 1

1.1 Background of Study 1

1.2 Motivation 4

1.3 Objectives 5

1.4 Scope of Research 6

1.5 Thesis Layout 7

CHAPTER 2 LITERATURE REVIEW

2.0 Introduction 8

2.1 Patchouli Essential Oil 8

2.1.1 Chemistry of Patchouli Oil 10

2.2 Patchouli Oil Extraction Techniques 13

x

2.2.1 Solvent Extraction 15

2.2.2 Water Solvent Extraction (Hydrodistillation) 18

2.3 Molecular Mechanics 19

2.3.1 Intramolecular Forces 21

2.3.2 Intermolecular Forces 21

2.3.3 Intermolecular Potential Energy 27

2.4 Molecular Dynamics Simulation 30

2.4.1 Force Field 33

2.4.2 Time Integration Algorithm 35

2.4.3 Periodic Boundary 35

2.4.4 Thermodynamic Ensemble 36

2.4.5 Analysis Parameter 37

2.5 Conclusion 40

CHAPTER 3 MATERIALS AND METHODS

3.0 Introduction 41

3.1 Materials 41

3.1.1 Dried Patchouli Leaves 41

3.1.2 Solvents 43

3.2 Solvent Extraction 44

3.2.1 Apparatus & Methodology 45

3.2.2 Gas Chromatography Mass Spectra (GCMS) Analysis 46

3.3 Molecular Dynamics (MD) Simulation 47

3.3.1 Software & Hardware 48

3.3.2 Simulation Setting Parameter Details 48

3.3.3 Simulation Input Creation Stage 50

3.3.4 Simulation Box Creation Stage 51

3.3.5 Forcite Simulation Running 52

3.3.6 Trajectory Output Analysis 53

3.3.7 Simulation Validation 54

3.4 Conclusion 55

xi

CHAPTER 4 RESULTS AND DISCUSSION

4.0 Introduction 56

4.1 Solvent Extraction Experiments 57

4.2 Solvent Extraction Simulations 64

4.2.1 Simulation Validation 65

4.2.2 The Solvent-solvent Interaction 68

4.2.3 The Solute-solute Interaction 72

4.2.4 The Solute-Solvent Interaction 73

4.2.5 Simulated Density, Temperature and Pressure Properties 76

4.3 Comparison Study of Simulation Works for Two Extraction Techniques 77

4.3.1 Simulation Validation 77

4.3.2 The Solvent-solvent Interaction 80

4.3.3 The Solute-solute Interaction 85

4.3.4 The Solute-Solvent Interaction 86

4.4 Temperature Effect on the Solvent Extraction Technique 88

4.4.1 The Solvent-Solvent Interaction 88

4.4.2 The Solute-Solute Interaction 90

4.4.3 The Solute-Solvent Interaction 91

4.5 Conclusions 93

5. CHAPTER 5: CONCLUSIONS AND RECOMENDATIONS

5.1 Conclusions 95

5.2 Recommendations for future works 97

REFERENCES 98

APPENDICES

A GCMS result

B List of publications

xii

LIST OF TABLES

Table No. Title Page

2.1 Patchoulol properties 12

2.2 Polar aprotic solvent categories and characteristics. 17

3.1 Properties of solvents used in the solvent extraction experiment. 43

3.2 Simulated systems applying the atom based summation method

for long-range interactions calculation. 49

3.3 List of simulated systems applying Ewald summation method. 50

3.4 Dynamic running stage details for both summation methods. 53

3.5 Force field that used during validation stages 55

4.1 The extraction yield of patchouli oil extracted using the solvent

extraction technique. 57

4.2 Comparison of extraction yield according to extraction technique

and study. 58

4.3 List of compounds detected by GCMS for sample extracted using

acetone as the solvent 59

4.4 List of compounds detected by GCMS for sample extracted using

ethanol as the solvent 61

4.5 List of compounds detected by GCMS for sample extracted using

hexane as the solvent 62

4.6 List of chemical compounds in patchouli essential oil which were

extracted by the organic solvents 63

4.7 Simulation results for patchouli oil extraction process. 76

4.8 Nonbonded Parameters, geometry, and electrostatic properties of

the TIP3P water model. 78

4.9 Comparison of patchoulol composition for both extraction techniques 83

xiii

LIST OF FIGURES

Figure No. Title Page

1.1 Schematic of the scope of study

7

2.1 The patchouli plant

9

2.2 Simplified skeleton of monoterpene and sesquiterpene

11

2.3 Patchoulol compound exists as enantiomers

12

2.4 Vacuum hydrodistillation appratus

18

2.5 Schematic representation of some of the important forces in

molecular mechanics calculation

20

2.6 Schematic of a dipole-dipole interactions

23

2.7 Example of H-bonding (a) weak, (b) intermediate and (c)

strong interactions

24

2.8 Illustration of polarization process

26

2.9 The induced dipole-dipole interaction of Helium with (a)

before and (b) after interactions

27

2.10 The van der Waals Lennard Jones potential for helium

interactions

28

2.11 General scheme of molecular dynamic simulation steps

32

2.12 Periodic boundary condition in two dimensions with

molecules free to cross the four edges

36

2.13 Schematic representation of rdf in fluid, probability of how

frequently the nearest neighbor atoms move along the

spherical radius, r. The dashed regions contribute to the first

and second coordination number shells respectively

39

2.14 The atomic configuration and rdf pattern for (a) gas, (b) liquid

and (c) solid phase

40

3.1 Patchouli leaves samples preparation flowchart

42

3.2 (a) Oven for sample drying and (b) Vibrating sieve shaker to

segregate leaves particle by size

42

xiv

3.3 Solvent extraction process flowchart

44

3.4 Vacuum rotary evaporator to separate the solvent from

patchouli essential oil

45

3.5 GCMS to identify the marker compound in the essential oil

46

3.6 Summarization of steps in MD simulation

47

3.7 Patchoulol molecule structure in 3D

51

3.8 Example of input box creation

52

3.9 Schematic labelling of patchoulol (a), acetone (b), ethanol (c),

hexane (d) water and (e) molecule structures

54

4.1 Comparison of rdf for O1A---O1A in pure acetone liquid

system from this study and Liang et al (2004) using

COMPASS and OPLS force field

66

4.2 Comparison of O1E---O1E in pure ethanol liquid system from

this study and Saiz et al (1997) using COMPASS and OPLS

force field

67

4.3 Comparison of C3H---C3H interaction in pure hexane liquid

system from this study and Kioupis et al (1999) using

COMPASS and TraPPE force field

68

4.4 Solvent-solvent interactions for pure and binary system with

hexane and acetone as the solvent

69

4.5 Solvent-solvent interactions in pure acetone and binary

acetone-patchoulol system

70

4.6 Solvent-solvent interactions for pure and binary systems

where ethanol as the solvent with the (a) attraction of O1E---

H1E and (b) repulsion of O1E---O1E are the intermolecular

interactions of interest

71

4.7 Solute-solute interactions in pure patchoulol system and

binary systems with O1P and H1P as reference atoms for

hydrogen bond interactions

73

4.8 Solute-solvent interactions in the binary ethanol-patchoulol

system

74

4.9 Solute-solvent interactions through interactions of O1A---H1P

(attraction; hydrogen bond) and O1---O1P (repulsion) in the

binary acetone-patchoulol system

75

xv

4.10 Solute-solvent interaction in the binary hexane-patchoulol

system with H3C (hydrogen atoms at both ends of hexane)

75

4.11 Comparison of O1W---H1W in pure water system using

COMPASS and TIP3P force field

79

4.12 Comparison of O1E---O1E in pure ethanol liquid system

using COMPASS and OPLS force field

80

4.13 Solvent-solvent interactions in pure water and binary water-

patchoulol system with(a) the attractive force via O1W--H1W

and (b) the repulsive forces due to O1W--O1W interactions

81

4.14 Solvent-solvent interactions in pure ethanol and binary

ethanol-patchoulol system with (a) the attractive force via

O1E--H1E and (b) the repulsive forces due to O1E--O1E

interactions

82

4.15 Snapshot of analyxed trajectory output for (a) hydro-

distillation (binary water-patchoulol system) and (b) the

solvent extraction (binary ethanol-patchoulol system)

after 1ns simulation time at 298K and 1 atm with COMPASS

force field

84

4.16 Solute-solute interactions in pure patchoulol and solvent-

patchoulol binary system represented by O1P---H1P

interaction (hydrogen bonding)

85

4.17 Solute-solvent interaction in (a) hydroditillation (binary

water-patchoulol system) and (b) solvent extraction (binary

ethanol-patchoulol system)

87

4.18 The radial distribution calculation to describe the attractive

forces in simulation of solvent extraction at different

temperature for both pure and binary systems. O1E---H1E

represent the hydrogen bonding interaction of solvent-solvent

molecules

89

4.19 Radial distribution calculation to describe the repulsive forces

in simulation of solvent extraction at different temperature for

both pure and binary systems

90

4.20 Solute-solute interaction results for both pure and binary

system at 298K and 303K

91

4.21 Rdf calculation to describe the attractive forces in the

simulations of solvent extraction at different temperature for

binary systems

92

xvi

4.22 Rdf calculation with O1P and O1E as reference atoms in

simulation of solvent extraction at different temperature for

binary system

92

xvii

LIST OF SYMBOLS

a Acceleration

y Density of y type atom

Estretch Energy bond stretch term

Eqoulumbic Energy Coulombic interaction

Ebend Energy angle term

Eout of plane Energy improper dihedral term

Etorsion Energy torsion term

Evan der waal Energy van der waals interaction

h Plank’s constant (6.626 x 10-34

m2kgs

-1)

υ Orbiting frequencies of electrons

ε Well depth

Ny Number of atoms of the y type

q Partial charges

α Polarisability

σ Collision diameter

Å Angstrom

Q Fictitious mass

V Potential energy

r Radius

l Bond length

ɷ Dihedral angle

θ Angle

ᵩ Torsion

m Mass

xviii

µ Dipole moment

πεo Permeability of vacuum

xix

LIST OF ABBREVIATION

2nd

Second

3rd

Third

μm Micrometer

atm Atmospheric pressure

CCRC Caritas Czech Republic Corporation

COMPASS Condensed-phase Optimized Molecular Potentials for Atomistic

Simulation Studies

DPPH 1,1-diphenyl-2-picylhydrazyl

fs Femtosecond

GCMS Gas Chromatography Mass Spectrometer

g(r) Probability valueof how frequently the nearest neighboring atoms move

along the spherical radius

kg Kilogram

LJ Lennard-Jones

MD Molecular dynamics

N Number of molecules

NIST National Institute of Standards Technology

NVE Constant number of moles, volume and energy ensemble

NPT Constant number of moles, pressure and temperature ensemble

NVT Constant number of moles, volume and temperature ensemble

ns Nano second

P Pressure

ps Pico second

OPLS Optimized Potential for Liquid Simulations

xx

R, r Radial

rdf Radial distribution function

T Temperature

TraPPE Transferable Potentials for Phase Equilibria

TIP3P Transferable Intermolecular Potential, Three-Position model

vdw Van der waals

wt Weight

wt/wt % Weight / weight percent

CHAPTER 1

6. INTRODUCTION

1.0 INTRODUCTION

This chapter discusses the general research background, motivation, objectives,

scope and the summary of thesis presentation. This study will investigate the suitability

of molecular dynamic simulation as a prediction tool in chemical engineering to

enhance the understanding of the extraction mechanism at the molecular level. The

general background will describe the materials of study and the molecular dynamic

simulation technique.

1.1 BACKGROUND OF THE STUDY

Malaysia has an abundance of native aromatic plants such as patchouli (nilam),

aloeswood (gaharu), jasmine (melur) and some other with its own natural scent

compounds which can be extracted as essential oils. These essential oils are

incorporated into cosmetic, perfumery and toiletries products. During January to April

2012, Malaysia imports about RM 1268 million worth of these essential oils and related

products (Malaysia Monthly External Statistic, 2012). Beside its natural scent, the

essential oil, also function as the natural antioxidant, aromatherapy agent and

additive/preservative agents (Burt, 2004; Celiktas et al., 2007; Dastmalchi et al.,2008).

2

The demands for natural products particularly essential oils continue to increase as more

customers believe that natural products are safer compared to artificial products. In

addition, the demand and awareness for green and eco-friendly products today have

further promoted the usage of natural scent compounds in cosmetics and toiletries.

Patchouli essential oil extracted from dried patchouli leaves, is well known for

its woody and earthy scent (Frater et al., 1998; Deguerry et al., 2006). The patchouli

scent has been incorporated in many cosmetic and perfumery products especially in

products for men due to their earthy and long lasting aroma characteristic (Raghu,

2006). An important marker constituent of the patchouli essential oil is patchoulol

(C15H26O). It is also the major compound in patchouli essential oil and has been used to

quantify the patchouli essential oil quality which is reflected in the essential oil market

price. The global demand for patchouli essential oil is estimated to be around 1600

tonnes annually (Raghu, 2006). Aside from the application of its scent, the patchouli

essential oil has also been investigated for various applications such as insect repellent

and fungicide application (Hybertson, 2007). Furthermore, the patchouli essential oil

has also shown valuable pharmacology potential (Miyazawa et al., 2000; Wei and

Shibamoto, 2007; Lu et al., 2011). In addition, the major compound of patchouli oil

(patchoulol) has also been explored for its application in the medical field such as

anticancer, antioxidant and antiviral properties (Kiyohara et al., 2012; Jeong et al.,

2013). The detail discussion on the application of patchouli essential oil is further

discussed in the next chapter.

The vast potential of patchoulol and patchouli essential oil in various

applications has indeed risen up the demand for patchouli essential oil production. The

price for patchouli essential oil in 2011 is estimated around RM600/kg (Fahlevi, 2011).

In addition, according to Nilam Aceh: A Study of the Patchouli Oil Industry in Aceh,

Indonesia; a book on marketing research on the patchouli plant in 2011 prepared by the

Caritas Czech Republic Corporation (CCRC); has reported that there is still a 600 to

800 tonnes gap between the supply and the world demand each year for patchouli

essential oil. Hence, it is expected that patchouli related industries in Malaysia such as

patchouli plant cultivation and essential oil production will probably expand especially

due to the suitability of patchouli to be cultivated in Malaysia with lower catastrophe

3

risk. Furthermore, up to this point, there is no synthetic technique that has been

established to produce patchouli essential oil or its marker compound (Deguerry et al.,

2006). Mulder-Krieger et al. (1988) reported that there were no free volatile

sesquiterpene compounds accumulated in callus and suspension cultures of the

patchouli plant from their study. This indicates that the expansion of patchouli related

industries will require continuous research activities mainly in the patchouli extraction

field to support the growth of demand.

In the patchouli essential oil production, the optimum condition which

contributes to the increased yield of patchouli essential oil during the extraction process

is gaining a lot of interest from researchers (Hybertson et al., 2007; Donelian et al.,

2009; Yahya, 2012). One of the possible exploration tools is through the computer

simulation which focuses on the molecular level interaction. This molecular level

simulation technique can reduce the amount of time on the research experimental work,

is more economical and environmentally friendly compared to the experimental study.

It also promotes a better understanding on interaction between molecules that can be

used to explain the mechanism of the extraction process and can be seen as a virtual

laboratory (Rapaport, 2004) at the molecular scale.

In this study, the computer simulation technique applied is the molecular

dynamics (MD) simulation. It is a powerful tool to help comprehend and reveal

intermolecular interaction behaviour between the solute and solvent molecules during

the extraction process (Maginn and Elliot, 2010). The solute in this study is patchoulol

as the major and marker compound in the patchouli essential oil. While the solvent used

is based on the chosen extraction technique, for example the water for hydrodistillation

technique. By applying Newton’s second law, the simulation will simulate the dynamic

aspect of the system. The coordinate system will be used to calculate the radial

distribution function (rdf), and diffusion coefficient which can be used to describe the

solvation strength towards patchoulol mass transfer behaviour during the extraction. It

is expected that the modelling results will be able to give an insight into how crucial

parameters can be controlled during the extraction process of patchouli oil, such as

solvent type and temperature.

4

1.2 MOTIVATION

The expansion of various industries such as food and cosmetic have amplified

the demand for value added natural products in particular patchouli essential oil. In

Malaysia, the market value for the essential oil industry is estimated to be around RM2

billion (Berita IDS, 2000) with the demand for it continuing to increase since the usage

has become wider. At present, the focus for most of the researches in the patchouli oil

extraction is on how to increase the production yield. For example it was done by

utilizing a different extraction technique such as hydro-distillation, solvent extraction

and other extraction techniques. However, there is a limitation of present studies which

is the inability to explain the interaction at the molecular level during the extraction

process, which is an important fundamental aspect to be recognized for optimum

process parameter such as solvent, temperature and others.

Thus, the core of this study focuses on understanding the molecular level

interaction and providing some molecular information such as solute solubility during

the patchouli oil extraction process. The molecular dynamic simulation was used to

simulate the molecular interaction of the extraction process. The exploration of the

interaction between the solute (patchoulol) molecules and the solvent molecules will

enlighten the interpretation of which atoms play a significant role in the interaction of

both solute (patchoulol) and solvent molecule. The interaction of solute (patchoulol)

and the solvent molecular interaction in the system will help to describe the extraction

process through the calculation of solubility parameter. Later, this data can be used to

predict the extraction behaviour of solute (patchoulol) using solvent extraction and

hydro-distillation method. This tool has been applied by Gunther et al. (2005) to predict

the extractability of Aesculus hippocastanum and Harpagophytum procumbent utilizing

super critical carbon dioxide extraction technique. They predicted the extracted yield

through calculation of solutes: (-)–α-Bisabolol, Aescin, Harpagoside and Stachyose

solubility in the pure and modified supercritical carbon dioxide solvent and have

concluded that molecular dynamic simulation can be used to predict the minimum

requirement for the supercritical carbon dioxide modifier to extract both lipophilic and

hydrophilic compounds.

5

In addition to fascinating molecular environment exploration, the limited studies

(Kongkathip et al., 2009; Fan et al., 2011) that used solvent extraction technique to

extract the patchouli oil had given further an encouragement for this study to apply this

extraction technique. In addition, both of the study publications applied the solvent

extraction to extract the patchouli essential oil which did not discuss gas

chromatography results in details. The GCMS is an important characterization because

it will determine the patchoulol composition and confirm the patchouli essential oil.

Therefore, this study will link GCMS results and estimate the quality of extracted

patchouli essential oil using the solvent extraction technique.

Solvent extraction offers various types of solvent with different properties and

characteristic which can be applied to have optimum production. One of the appealing

concepts is the ability of the solute (patchoulol) to establish the hydrogen bonding with

the solvent molecules through its hydroxyl functional group. The hydrogen bond is the

strongest intermolecular interaction that is stable and has given the unique properties of

water. It is expected the intermolecular interaction will affect the solubility solute in the

solvent and then influence the extraction yield which is dependent on the solution

chemistry (Adam, 2012). The solution chemistry can be characterised through

intermolecular interaction which rely on the solvent properties.

1.3 OBJECTIVES

The main motivation for this study is to gain a fundamental understanding of the

molecular science during the patchouli essential oil extraction process as there is avoid

in literation on reported work on the usage of this simulation technique to visualize the

solute solubility during patchouli extraction process. The key objective of this study is

to recognize the intermolecular interaction which is a significant factor influencing the

patchouli essential oil extraction process and yield. Furthermore it is interesting to

figure out how the simulation work and extraction experiment results can complement

each other. Good simulation results will support the extraction experiment results and

would be able to describe the process. Therefore this study was embarked upon with the

following objectives;

6

a. To recognise the type of intermolecular interaction has significant effect

during the patchouli extraction which was produced via molecular dynamic

simulation technique. The simulation will measure the intensity of

intermolecular interaction between the solute and the solvent which reflect

the solubility of the solute molecules in the solvents.

b. To examine the linkage between simulation work and extraction experiment

results to figure out the suitability of the molecular dynamic simulation

technique as a prediction tool. Simulation results which in accordance with

the extraction experiment results could be used to describe the

intermolecular interaction during the extraction process. Furthermore, it is

interesting to discover how well the simulation of the chosen solute would

be able to describe intermolecular interaction compared to combination of

solutes.

c. To determine which solvent can extract the highest patchouli essential oil

yield and support with the simulation results as molecular evidence.

d. To examine the prediction capability through simulation at different

temperatures since the molecular environment is sensitive to temperature

variation.

1.4 SCOPE OF THE STUDY

This study is divided into two main tasks in addressing the objectives. The tasks

are the simulation study and the experimental works. The simulation study will

determine the molecular interaction during the experimental process. Both of the task

results should be parallel and supporting each other. Therefore, the experimental results

can be used as validation of the simulation works which would help to determine the

suitability of the simulation technique as a prediction tool.

Generally, the simulation study will investigate two main factors which are the

solvent types and temperature effect. While the extraction experiments with different

type of organic solvents will produce the extraction yield and then will be correlated

with the simulation result. The schematic illustration of the scope of the study is

summarised in Figure 1.1.

7

Figure 1.1: Schematic of the scope of study.

1.5 THESIS LAYOUT

This chapter discusses the background information and the significance of the

research motivating this study. It also describes the study limitation through the research

scope. Chapter Two, further elaboration on the literature review of this study is detailed

out. The focus material (patchouli essential oil) chemistry, extraction technique used

and the detailed on simulation technique is described in this chapter. In Chapter Three a

detailed description of the methodology of simulation study and extraction experiments

are defined. The results and discussions are presented in the Chapter Four. It discussed

solvent extraction experiment and simulation study results, the comparisons between

simulation for hydrodistillation and solvent extraction with ethanol as the solvent and

the simulation results for simulation at different temperature (298K and 303K) in

ethanol as the solvent. The conclusion of the study and some suggestions with

recommendations for future works is described in Chapter Five.

Patchouli Extraction Process

Experimental works Simulation study

Acetone

Hexane

Analysis of

product GCMS

Extraction

experiment using

solvent extraction

Solvent extraction Hydrodistillation Ethanol

Polar Non-polar:

Hexane

Acetone Ethanol

Simulation for

Temperature variation:

298K and 303K

CHAPTER 2

7. LITERATURE REVIEW

2.0 INTRODUCTION

The aim of this chapter is to review the fundamental science of the extraction

process and the simulation technique. It begins with the description of the patchouli

essential oil as the study material. This includes the properties of the patchouli essential

oil and the compound in the patchouli essential oil that will be used as the target

molecule in the simulation. This is followed by the discussion on the extraction process

that was used to produce the patchouli essential oil. This chapter also defines the

underlying principle of molecular mechanics which is the main concept behind the

molecular dynamics (MD) simulation. In addition, the properties such as radial

distribution function (rdf) and hydrogen bond formation is explained as they are

relevant to the experimental work and simulation study output.

2.1 PATCHOULI ESSENTIAL OIL

Patchouli essential oil comprises of mostly terpenoids. It is extracted from the

patchouli plant or Pogostemon cablin Benth (Figure 2.1). The patchouli plant belongs to

Laminacaeae family originating from the Philippines, Malaysia and India (Raghu, 2006;

Hu et al., 2006). The oil gland which containing terpenoids is located on the underside

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of the patchouli leaves (Rhind, 2012) and has been identified by Holmes in

1986 (Raghu, 2006). The current top world producer of patchouli essential oil is

Indonesia with production estimated around 80 to 90% of global demand which is

around 1200 to1400 metric tonnes per year (CCRC, 2011). The patchouli essential oil is

being appreciated for its pleasant odour which is contributed by its major compound

which is patchoulol or patchouli alcohol (Deguerry et al., 2006). Researchers in the

fragrance field describe the odour as woody and earthy odorants and one of the natural

sources with this characteristic (Frater et al., 1998).It is normally incorporated into

heavy perfumes due to its longer lasting properties besides its application in cosmetic

and toiletries (Raghu, 2006).

Figure 2.1: The patchouli plant

Source: Rukmana (2003)

Other than its attractive woody scent (Naf et al., 1981), the patchouli essential

oil possesses various types of pharmacological benefits such as antidepressant,

antioxidant, anti-inflammatory, antiseptic, antifungal (Hybertson, 2007; Miyazawa et

al., 2000; Ichikawa et al., 1989). In Chinese traditional medicine, the patchouli essential

oil is used to treat dyspepsia, vomiting, diarrhoea and poor appetite (Yang et al., 1999)

as well as to “remove dampness” (Fan et al., 2011). An earlier study by Lapin and