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European Journal of Applied Sciences – Vol. 9, No. 5
Publication Date: October 25, 2021
DOI:10.14738/aivp.95.10897. Koffi, K. A., N’Guessan, B. R., & Bamba, E. H. S. (2021). The Phospholipid Degradation in Paddy Rice: A Theoretical Model with
DFT/B3LYP 6–311 G. European Journal of Applied Sciences, 9(5). 162-174.
Services for Science and Education – United Kingdom
The Phospholipid Degradation in Paddy Rice: A Theoretical
Model with DFT/B3LYP 6–311 G
Kouassi Alain Koffi
Laboratoire de Constitution et Réaction de la Matière
UFR SSMT, Université Félix Houphouët Boigny
22 BP 582 Abidjan 22, Côte d’Ivoire
Boka Robert N’Guessan
Laboratoire de Constitution et Réaction de la Matière
UFR SSMT, Université Félix Houphouët Boigny
22 BP 582 Abidjan 22, Côte d’Ivoire
El Hadji Sawaliho Bamba
Laboratoire de Constitution et Réaction de la Matière
UFR SSMT, Université Félix Houphouët Boigny
22 BP 582 Abidjan 22, Côte d’Ivoire
ABSTRACT
This work focuses on the degradation of phospholipids during rice storage. It aims
to identify the chemical phenomena underlying this process. It aspires to test the
hypothesis that 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (PC) triggers
the latter. It uses the Density Functional Theory (DFT) at the B3LYP/6–311 G level
in this sense. The research evaluates the reactivity of phospholipids; it estimates
the orbital frontier energies. It assesses its global index. It determines the dual
descriptors. It measures the molecular electrostatic potential. It calculates the
thermodynamic quantities related to phospholipids formation. It discusses these
results before concluding. The energies of the orbital frontier establish that 1-
palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (PE) is more reactive than
PC. In other words, PE is the precursor of lipid alteration. The work highlights the
parts of PE likely to join this transformation. This research demonstrates that PE
reacts with its C=O (sp2) or C-O (sp3)-C oxygen or its phosphorus P2 when it
associates with a nucleophilic entity. For an electrophilic attack, it interacts with its
hydrogen and its nitrogen or its C92 carbon (sp2). These sites can promote its
deterioration during rice storage.
Keywords: Phospholipids, paddy rice, chemical reactivity, dual descriptor
INTRODUCTION
Ivorians have been consuming rice for a long time. Côte d’Ivoire is struggling to meet its needs
for this product. Moreover, it manages to use only about 50% of the harvest. It suffers huge
losses. Food spoilage constitutes a major concern of the research team in recent years. It
concerns the banana [1,2] and the rice [3]. Their sustainable conservation contributes to
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Koffi, K. A., N’Guessan, B. R., & Bamba, E. H. S. (2021). The Phospholipid Degradation in Paddy Rice: A Theoretical Model with DFT/B3LYP 6–311 G.
European Journal of Applied Sciences, 9(5). 162-174.
URL: http://dx.doi.org/10.14738/aivp.95.10897
achieving food security in Côte d’Ivoire. A considerable proportion of the population consumes
them [4].
This work extends an unprecedented paper on the degradation of disaccharides or
trisaccharide [3] in rice. The latter proves that amylose under the action of water dissociates
into disaccharides. On the other hand, the lipids in rice also change. In colorimetry and
differential scanning calorimetry studies [5,6] and high-performance liquid chromatography
[7,8] shows that these molecules metamorphose during storage. The quality of phospholipids
appreciably alters [9,10]. Liquid extractions in a mixture of solvents following an accelerated
aging process of rice at a temperature of 45 °C corroborate this metamorphosis [11]. More, the
organoleptic characteristics of rice are significantly affected through long storage at 30 °C while
at -20 °C they’re safeguarded across storage [12].
These compounds contain covalently bound phosphates and lipids. They form one major
classes of these litters [13]. They include mostly 1-palmitoyl-2-oleoyl-sn-glycero-3-
phosphocholine (PC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (PE) and 1-
palmitoyl-2-oleoyl-sn-glycero-3-phosphoinositol (PI). Their studies represent different
challenges.
These phospholipids impact directly on human nutrition and health [14,15]. Their beneficial
effects incorporate coronary heart disease, cancer or inflammation [13]. The start of the lipid
degradation process in rice during storage persists unknown. According to [7], PC starts the
degradation; the PC and PE proportion fall by 8.3% and 2.3% respectively. The proportion of
PI increases by 2.1%. These results ignore the reactions underlying these transformations. This
research focuses on the properties of phospholipids; it aims to provide a description of their
reactivity. It targets to specify the order of phospholipids degradation using quantum
mechanical tools. It determines bound orbital energies, global reactivity index and
thermodynamic quantities.
The analysis of these quantities suggests that PE be the precursor of lipid alteration. This result
refutes the thesis that the PC plays this role. Furthermore, the study focuses on dual descriptors
and the molecular electrostatic potential. These aspects help to identify the regions or sites of
PE that likely react during its transformation. This work conjectures that the phosphorus P2
and the oxygen of C=O (sp2) or C-O (sp3)-C associate with the nucleophiles. Its C92 (sp2) carbon
favours reactions with electrophilic entities. This article obeys the plan below.
Its materials and methods section follows this introduction. It details the calculation of bound
orbital energies and global reactivity index. It presents the dual descriptors and the molecular
electrostatic potential. It explains the thermodynamic quantities related to the formation of
phospholipids. The third section discusses the results. It reviews these statistics and their
interpretations. It precedes the conclusion. Figure 1 describes the structures of the three main
phospholipids in this study. It introduces its materials and methods.
MATERIALS AND METHODS
This study uses the DFT [16,17]. The Gaussian 09 quantum chemistry software hosts it [18]. Its
efficiency in predicting experimental data justifies its choice [17,19,20]. It optimizes the
standard geometrical parameters of the three phospholipids at the DFT level by the B3LYP
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functional [21] with the 6–311 G basis set. The vibration frequency calculation grants to
validate these results. These provide the energies of the highest occupied molecular orbitals
(HOMO) and the lowest vacant (LUMO). They estimate the electronegativity (χ) [22], the
hardness (ɳ) [23], the softness (S) [24], the chemical potential (μpot) [25] and the electrophilic
index (ω) [26]. The present work focuses on phospholipids descriptors that account for their
reactivity.
Descriptors of reactivity
This section deals with global and chemical potential dual index. The energies of HOMO and
LUMO, electronegativity (χ), hardness (ɳ), softness (S), chemical potential (μpot) and
electrophilic index (ω) describe the reactivity of a phospholipid.
Molecular orbital bounds and global index of reactivity
The Koopmans approach framework helps determine Ionization potential (EIP) and electron
affinity (EA) [27]. It calculates from the following relationships:
�!" = −�#$%$ ��� �� = −�&'%$ (1)
μ()* = − +!",+-
. = − � (2)
ɳ = /
0 = +!"1+-
. (3)
ω = 2#
.ɳ (4)
Fig. 1. Structures of the three main phospholipids
The orbitals bound play an important role in the qualitative interpretation of chemical
reactivity [28]. The HOMO connects directly to the ionization potential EIP. The LUMO associates
with the electronic affinity (EA). Their energy difference (Δε) distinguishes them. A
phospholipid with a high energy gap (Δε) becomes low polarized. Its activity remains weak and
its kinetic stability increases [29]. Moreover, this compound reacts more as its chemical
O
O O P
O
O
CH2
CH2 N
O H
O
CH3
CH3 CH3 O- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (PC)
O
O O P
O
O
CH2
CH2 NH3 O H
O
O- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (PE)
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European Journal of Applied Sciences, 9(5). 162-174.
URL: http://dx.doi.org/10.14738/aivp.95.10897
potential (μpot = -χ) remains low. The dual descriptor identifies how the parts of a molecule
contribute to its chemical reactivity.
Dual descriptor
The “dual descriptor” of reactivity helps to detect electrophilic and nucleophilic regions in a
molecule [30,31]. Its use presents an advantage over the Fukui index [32]. These are for one
site only. The statistic ∆f builds on the Fukui functions. The follow relationship helps to calculate
these:
∆�(�) = [�4
, − �4
1] (5)
Where �4
, et �4
1 denote the Fukui function for a nucleophilic and electrophilic attack
respectively.
∆�(�) > 0 indicates an electrophilic region. The latter becomes favourable to a nucleophilic
attack. However, if ∆�(�) < 0, it suits for reaction with an electrophilic entity. Moreover, the
Fukui functions come from the distribution of Hirschfeld’s population [33]. The following
section explains this aspect.
This decision justifies by the important role played in the molecular systems study by the
Hirschfeld atomic charge calculation [34]. To describe quantitatively its distribution, the latter
suggests dissecting the chemical unit into well-defined atomic fragments. A natural choice
shares the charge density on each point between the different atoms: this distribution
resembles those of the latter. These remain free at the corresponding distances from the nuclei
[33]. Load density identifies the distribution of Hirshfeld populations. It allows discussing the
molecular electrostatic potential (ESP).
Molecular electrostatic potential
ESP helps to determine the preferred sites for electrophilic and nucleophilic attacks. It indicates
that which suits to establish hydrogen bonds. Its representation includes jointly the shape, the
size and that of the molecules in terms of colour regression. For several authors [35,36,37], the
map of this ESP facilitates the identification of correlations between structures and their
physicochemical properties. This work also evaluates thermodynamic parameters of
phospholipid formation.
Thermodynamic parameters of the formation
The enthalpies, free enthalpies and entropy of formation are those exploited here. The formulas
of Otchhersky permits to calculate them [38]. The first one is corrected using Jana values [39].
These formulas are as follows:
∆�5
6(�, 0�) = ∑ �7 ∆5�6
9:;<= (�, 0�) − ∑ �6(�) (6)
∆�5
6(�, 298�) = ∆�5
6(�, 0�) + (�%
6 (298�) − �%
6 (0�) − ∑ �(�>
6
9:;<= (298�) − �>
6(0�) )
(7)
where ∑ �6 = ∑ ��6 − �6(�) + �?"+ (8)
and �%
6 (298�) − �%
6 (0�) = �@;;A − �?"+(�) (9)
�@;;A − �?"+(�) represents the correction of the molecule’s enthalpy. ∑ �6 , �6(�) �� �?"+
correspond respectively to the atomic energy, to the total energy of the molecule and that of its
zero points. X represents the element and � its number in the molecule.
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The enthalpy correction for the atomic element obtains with the relation �>
6(298�) − �>
6(0�).
The calculations relating to the entropy and the free enthalpy of formation use the relations
(10) and (11). The exploitation of these sizes leads to various results.
∆�5
6(�, 298�) = �% − ∑9:;<= �∆�(298�) (10)
∆�5
6(�, 298�) = ∆�5
6(�, 298�) − �∆�5
6(�, 298�) (11)
RESULTS
This section presents the results obtained for the molecular electrostatic potential (ESP) and
thermodynamic parameters. But first, it focuses on those of the reactivity descriptors.
Molecular orbitals bound
The table 1 shows the values of the phospholipids HOMO and LUMO frontier orbital’s energies
obtained at the level of theory B3LYP/6-311G. The following part concerns the global reactivity
descriptors.
Table 1. Values of the phospholipids HOMO and LUMO frontier orbital’s energies
Compounds �����(��) �����(��) ��(��) ���(eV)
PC -6.263 -0.759 5.504 6.263
PE -6.439 -1.318 5.121 6.439
PI -6.409 -1.044 5.365 6.409
Global reactivity index
Table 2 collect the values of global reactivity descriptors of the three main phospholipid. The
following section summarizes those of the dual descriptor and the molecular electrostatic
potential.
Table 2. Global reactivity descriptors of the three main phospholipid
� (eV) � (eV-1) ����(��) � (eV) � (��) μ(Debye)
PC 3.511 0.364 -3.511 2.752 2.240 20.41
PE 3.879 0.390 -3.879 2.561 2.938 7.69
PI 3.727 0.373 -3.727 2.683 2.589 7.25
Dual descriptor and molecular electrostatic potential
Tables 3 and 4 gather the values of the dual descriptor from the FUKUI index and those of the
electrostatic potential respectively. Moreover, the last results concern the thermodynamic
quantities of PE, PI and PC formation.
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Koffi, K. A., N’Guessan, B. R., & Bamba, E. H. S. (2021). The Phospholipid Degradation in Paddy Rice: A Theoretical Model with DFT/B3LYP 6–311 G.
European Journal of Applied Sciences, 9(5). 162-174.
URL: http://dx.doi.org/10.14738/aivp.95.10897
Table 3. Values of the PC, PI and PC local index and the dual Fukui descriptor
Atoms ��
, ��
- ∆��
Phospholipid PC
C31 -0.091 4 -0.003 7 -0.087 7
C91 -0.088 6 0.000 6 -0.089 2
C123 -0,003 8 -0,047 6 0,043 8
C131 -0,003 6 -0,050 3 0,046 7
Phospholipid PI
P2 0.031 3 -0.053 4 0.084 7
O3 -0.002 8 -0.021 3 0.018 4
O13 -0.015 7 -0.016 1 0.000 4
C15 -0,003 7 -0,082 2 0,078 5
O16 -0.008 7 -0.060 1 0.051 3
C31 -0.106 6 -0.012 3 -0.094 3
C92 -0.105 3 -0.006 9 -0.098 4
C94 -0.018 9 -0.002 0 -0.016 9
C97 -0.018 8 -0.003 1 -0.015 7
Phospholipid PE
P2 -0.005 6 -0.119 6 0.114 0
O4 -0.004 5 -0.034 0 0.029 6
C5 -0.001 4 -0.025 2 0.023 7
C31 -0.094 9 -0.003 7 -0.091 2
O84 -0.002 4 -0.072 1 0.069 7
C92 -0.094 0 0.002 1 -0.096 1
C94 -0.016 8 -0.000 9 -0.015 9
C97 -0.016 6 -0.000 5 -0.016 2
Table 4. Summary of analysis related to the Dual Descriptor and electrostatic potential
Phospholipids Dual descriptor
Electrophilic sites Nucleophilic sites
PE P2 C92 (sp2)
PC C131 C91 (sp2)
PI P2 C92 (sp2)
Molecular electrostatic potential
PE
� = � (sp2) and C-O(sp3)-C Hydrogen and nitrogen PC
PI
Thermodynamic quantities of PI, PE, and PC formation
Table 5 shows the changes in enthalpies, free enthalpies and entropy associated with the
formation of the major phospholipids in rice. The following section discusses them.
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Table 5. Thermodynamic quantities of PI, PE and PC formation
Compounds ∆��(����. ���-�) ∆��(����. ���-�.�-�) ∆��(����. ���-�)
PI -4034.830 -3.980 -2848.262
PE -3276.609 -3.553 -2217.380
PC -3425.152 -3.821 -2285.954
DISCUSSION
This section details the cases of the molecular electrostatic potential (ESP) and the
thermodynamic parameters for the PC, PE, and PI compounds in Figure 2. Before, it focuses on
the descriptors of reactivity.
Descriptors of reactivity
The descriptors of phospholipid reactivity relate to molecular orbital bounds, global reactivity
index and dual descriptors. The next part explains the reactivity of phospholipids from the
orbital frontier energies and the gap obtained.
Molecular orbitals bound
The energies of HOMO are in the same order of magnitude. Nevertheless, the difference of 0.176
eV between the PE and PC HOMO is enough to assert that the latter becomes more adept at
donating electrons than the former.On the other hand, PE equals its lowest value (εLUMO = -1.318
eV). It’s potentially the electron acceptor. The data on HOMO and LUMO energies agree on the
latter assertion. A phospholipid with a high gap (Δε) polarizes with difficulty. Its activity
remains weak, and its kinetic stability increases [29]. The data in Table 1 indicate that the
energy gap varies as follows
��(PE) ˂ ��(PI) ˂ ��(PC).
PE represents the lowest value of Δε (Δε = 5.121 eV). It’s the most polarizable. Its chemical
reactivity subsists high, and its kinetic stability stays minimal [32]. On the other hand, PC
corresponds to the maximum of Δ� (Δ� = 5.504 eV). PC polarizes difficulty. Its activity decreases
and its stability increases [29]. PI accepts and gives the electrons. Its energy is between those
of PE and PC. Its polarizability, reactivity and stability remain average. The reactivity of these
phospholipids depends on that of its global index.
Global reactivity index
Table 2 shows the highest values of electronegativity (χ = 3.879 eV) and electrophilic index (ω
= 2.938 eV). These values indicate that PE corresponds to the best electron acceptor. This
phospholipid becomes the most oxidizable of the three. Other data in this table 2 corroborate
the results obtained with the molecular orbitals bound. PE also represents the most reactive;
its chemical potential (μpot = - 3.879 eV) or its chemical hardness (η=2.561 eV) stays the lowest.
Indeed, a compound reacts even more as its chemical potential (μpot = -χ) remains low. The dual
descriptor also helps to identify the reactive sites of its phospholipids.
Dual descriptor
The dual descriptor allows specifying the different atoms involved in the reactivity of
phospholipids. Table 3 gathers its PC, PE and PI values. Its data only concerns those of the
HOMO or LUMO. These prefer nucleophilic or electrophilic sites depending on Δfk.
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Koffi, K. A., N’Guessan, B. R., & Bamba, E. H. S. (2021). The Phospholipid Degradation in Paddy Rice: A Theoretical Model with DFT/B3LYP 6–311 G.
European Journal of Applied Sciences, 9(5). 162-174.
URL: http://dx.doi.org/10.14738/aivp.95.10897
The Δfk analysis establishes that the lowest values correspond to the C91 (sp2) PC and C92 (sp2)
PI or PE atoms. The latter indicate the select nucleophilic sites. Any attack of an electrophilic
group carries out in priority on them. The highest dual descriptors coincide with PC. Carbon
C131 and phosphor P2 of PE or PI. These atoms become the favoured electrophilic sites; any
reaction with a nucleophilic entity concerns them in priority. These results suggest the
modalities of phospholipid degradation.
The action of a nucleophilic entity with the PE or PI affects the P2 while that of an electrophilic
element realizes with the C92 initially. For PC, the first reaction is sited on the C91. The second
one starts on the C131 mainly. More, research mobilizes the molecular electrostatic potential
(ESP). This quantity helps to identify the reactivity of the phospholipid sites.
Molecular electrostatic potential
This section discusses the reactivity of the compounds based on the electrostatic potential map
obtained. Figure 3 shows the 3D graphical representations of the phospholipid ESP. The
different colours on the surface of each molecule indicate its sign. Red corresponds to its
negative value or to an electrophilic region. Blue materializes a positive statistic or a
nucleophilic zone. Green describes a neutral site. The ESP increases in the following order: red
˂ orange ˂ yellow ˂ green ˂ cyan ˂ blue ˂ white [40].
The different colours of the ESP map shows that the negative values are around the oxygen C=O
(sp2) and C-O (sp3)-C). These regions become electrophilic or protonation zones. The positive
potential (cyan to white) remains close to the hydrogen and nitrogen.
Table 4 summarizes the results of the analyses for the dual descriptor and the molecular ESP.
The first ones highlight the nucleophilic and electrophilic sites of phospholipids. Those of PE
equal PI. This indicator pinpoints their electrophilic sites in P2. Their nucleophilic sites are at
C92 (sp2). For PC, C131 represents the electrophilic site. Its nucleophilic site is in C91 (sp2).
For all lipids, the ESP situates the electrophilic sites on the oxygen C=O (sp2) or on C-O(sp3)—
C. The ESP casts them around the hydrogen and nitrogen.
These results provide information on where phospholipids can interact through intermolecular
or intramolecular bond. A nucleophilic entity reacts with their oxygen C=O (sp2) or C-O(sp3)—
C. For PE or PI, it can bind to phosphorus P2. For PC, it clings to the carbon C131. Electrophilic
species associate with its hydrogen and its nitrogen. For PE and PI, it interacts with the carbon
C92 (sp2). It connects to the PC through C91 (sp2). The following section focuses on
thermodynamic quantities to create PI, PE and PC.
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Fig. 2. Optimized structures of PI, PC and PE phospholipids
Optimized phospholipid PC
Optimized phospholipid PE
Optimized phospholipid PI
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Koffi, K. A., N’Guessan, B. R., & Bamba, E. H. S. (2021). The Phospholipid Degradation in Paddy Rice: A Theoretical Model with DFT/B3LYP 6–311 G.
European Journal of Applied Sciences, 9(5). 162-174.
URL: http://dx.doi.org/10.14738/aivp.95.10897
Fig. 3. Distribution of PC, PI and PI Phospholipids molecular electrostatic potential.
Phospholipid PC
Phospholipid PE
Phospholipid PI
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Thermodynamic quantities of PI, PE and PC formation
Table 5 shows that these quantities size all negative; they suggest that they possibly constitute
with a heat release. The standard enthalpy variations of formation suggest the order of
phospholipids stability. PI represents the most stable. PE constitutes the most reactive PC is
between the two. The latter becomes the predominant compound in the spherosome
membrane of rice. Based on this proportion, [7] indicates that it first degrades by
phospholipase D. After six months of storage, this compound remains in the majority. PC and
PE contents decreased by 8.3% and 2.3% respectively, while PI content increased by 2.1%. The
increase of the PI over time suggests the possibility of mutation. On the other hand, no direct
conversion links from PC to PI or from PE to PI or from PE to PC. However, these molecules
could degrade independently of each other. This information empowers to identify the
underlying modalities of lipid degradation.
CONCLUSION
Research aims to understand the chemical reactions underlying the degradation of lipids. It
wants to identify the extent to which PC plays a precursory role. Analyses of the molecular
orbitals bound energies show that the PE compound has the highest reactivity. PE becomes the
best electron acceptor or the most electrophile. Its kinetic stability stays the lowest. PE
represents the most reactive while PI remains the least one of the three phospholipids. PC is
between these two phospholipids. These observations make it possible to highlight the
reactions at the base of the lipid’s deterioration.
This work proves that the degradation results mainly from the degradation of PE. In other
words, the alteration of lipids would start with PE; the latter reacts more easily than PC. More,
this research concerns the sites of phospholipids likely to promote the PE deterioration.
Subjected to a nucleophilic entity, PE reacts with its �=� (sp2) or its �− � (sp3) −� oxygen. It
binds with its phosphor P2. For an electrophilic attack, it interacts with its hydrogen and its
nitrogen. It also uses its carbon C92 (sp2). This result explains the underlying reactions to rice
degradation. It offers a track limiter for this process. She suggests that mastering the reactivity
of PE can help.
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