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
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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