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In silico Modeling of Pectin-Based Superabsorbent Polymer Cross-Linked by CaCl₂, CaSO₄,

and Polyacrylamide

Blue S. Delos Santos

Pacita Complex National High School

Mary Jean Sabanal

October 19, 2022

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Drought is a prolonged dry period in climate, usually between April and September. One

of the major causes of drought is the occurrence of abnormal changes in weather patterns where

little to no rainfalls happen in a particular region. This can also transpire due to soil moisture

levels, supply and demand of water, land and water temperatures, and air circulation (Restuccia,

2016). When a certain area lacks precipitation, the soil gets much less moisture. Over time, this

phenomenon can cause the flow of streams to decrease and lead to insufficient water levels in

reservoirs. However, droughts do not only take place in hot, dry places. According to the World

Health Organization (WHO), approximately 55 million people globally are affected by droughts

annually. This influences the hazard in livestock, crops, food and nutrition, livelihood, air

quality, sanitation, and hygiene, increasing the risks of death and fueling mass migration (CDC,

2020). Moreover, water scarcity impacts 40% of the world’s population, this includes 700

million people who are at risk of being displaced as a result of drought by the year 2030. Such

disaster stresses reduce leaf size, stem extension, and root proliferation, disturb plant water

relations, and reduce water-use efficiency (Farooq et al.). In 2019, the Philippines experienced

drought due to an El Niño episode. It forced at least ten provinces in Mindanao to declare a state

of calamity (The Manila Times, 2022). Rainwater harvesting, ground surface water harvesting,

water conservation, reforestation, soil conservation, and early warning systems are some of the

modern solutions proposed for dealing with droughts (Omar et al., 2022).

Superabsorbent polymers (SAPs) or hydrogels are three-dimensional, cross-linked

networks of flexible polymer chains that carry dissociated ionic groups. They are materials that

can absorb aqueous solutions greater than 15 times their dried weight (Kiatkamjornwong, 2007).

They can absorb liquids such as water, synthetic urine, electrolyte solution, brines, and other

biological fluids. SAPs have been present since the 1950s and serve many functions ranging
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from hygiene products to construction and agricultural use. SAPs have water retention capacity

which can help with the stress of drought. Moreover, it can act as a reservoir holding on the

nutrients and can be used as a seed coating to increase seedling survival during water-limiting

conditions, like droughts (De Barros, Pimentel, & Araujo, 2017). The most highly used

superabsorbent polymer to date is sodium polyacrylate. It is a type of SAP used in making

disposable diapers, napkins, and other sanitary products. Although sodium polyacrylates are

proven to not be readily biodegradable.

The researcher will utilize In silico modeling through molecular simulation to identify the

best cross-linker of pectin in terms of water absorbency. Higher hydrophilicity means a stronger

affinity for water, thus being best suited as a superabsorbent polymer.

Background of the Study

Pectin is a polysaccharide consisting mainly of esterified D-galacturonic acid chains

found in fruits, specifically rich in the rinds of apples and citrus fruits (Aronson, 2016). Its

chemical formula is C₆H₁₀O₇. Pectin has been a well-known ingredient in the food industry

such as fat or sugar replacers in making frozen foods, jellies, and other low-calorie foods. There

are two types of pectin: High methoxyl (HM) Pectin and low methoxyl (LM) Pectin. HM is

usually labeled as "fast-set" or "slow-set" which is fitting in making chunky jams. In contrast,

LM is labeled as "light" and is used in making low-sugar recipes (Timberlake, 2022). Other

applications of pectin include making paper substitutes, foams, edible films, and plasticizers.

Although pectin is extensively used due to its gelling agent, only a few studies have conducted it

as a base constituent in making SAP.

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Superabsorbent Polymers (SAP) are a polymeric chain of networks that do not dissolve in

water but swell relative to the amount of solution (Behera & Mahanwar, 2019). It has been

prominent in various applications namely thermal energy storage, biosensors, tissue engineering,

drug delivery, and agriculture. Some polymers are stretched like rubber and polyester. SAPs can

be classified into two: synthetic or chemical-based, and natural or polysaccharide-based. These

SAPs have different mechanisms to work, (a) by changing their crystal structure and (b) by

physical entrapment of water by capillary forces. (c) a combination of mechanisms one and two,

and (d) a combination of mechanisms one and two coupled with dissolution and expansion of

chains limited by cross-linkages.

Calcium Chloride (CaCl₂) is an ionic compound of calcium and chlorine. It has a

molecular weight of 110.98 g/mol and a melting point of 772°C. It is hygroscopic in nature and

is soluble in water. CaCl₂ is used in the production of activated charcoal, used as electrolytes in

drinks, dust control, deicing, oil well drilling, and road stabilization (Garrett, 2004). According

to Micro-pak (2021), calcium chloride can absorb up to 300% of its weight.

On the other hand, calcium sulfate (CaSO₄), also known as gypsum, is an inorganic

compound that has a molar mass of 136.14 g/mol and a melting point of 1,460°C. It is usually

used as a desiccant, a tablet excipient, medicine for immobilizing casts, and as an impression

material in the field of dentistry. This is a highly active material that can absorb moisture from

the atmosphere.

Lastly, polyacrylamide (C3H5NO)n is a linear water-synthetic polymer and is described as

a combination of acrylic acid and acrylamide. This compound has a wide range of applications—

e.g., agriculture, food processing, pulp and paper production, mining, etc. (Doble & Kumar,
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2005). It is also present in some products such as lotions, color cosmetics, sunscreens, and facial

moisturizers. SEM Analyses showed that commercial hydrogels were likely a byproduct of

polyacrylamide (PAAm) and they were able to retain moisture for only a couple of hours

(Sangjoon et al., 2010).

“In silico” is a modern term that refers to a computer simulation performed via computer

software. Through the years, in silico models have been increasingly popular. This accounts to

be related to in vitro and in vivo models as one can perform experiments within their reach. It is

much cheaper, faster, and safer (Badano, 2021). It is quick since the computational time is short,

and it can solve large-scale problems. In silico methods include databases, homology models,

molecular modeling approaches, data mining, machine learning, and data analysis tools (Ekins,

2007). It can be utilized in a vast variety of biological research projects, including medicine

development, food toxicity testing, and cosmetics production. In silico simulations are also used

to virtually predict how a compound will react with proteins in the body or with pathogens

(Whiting, 2021). In silico software are Clustal X, Chimera, I-TASSER, PyMol, AutoDock Vina,

Primer-BLAST (Primer3), Geneious Prime, and more (Amnah Fawad 2021). Molecular

modeling and simulations refer to computational approaches that are used to observe dynamics,

thermodynamics, macromolecular structure, and microscopic material properties. Molecular

simulations are a well-known discovery method in science and engineering, with applications

spanning from medication development to materials design. The accuracy and reliability of the

specified force fields determine the fidelity of molecular simulation predictions (Cailliez et al.

2020).
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Statement of the Problem

The researcher aims to determine the best cross-linker to a pectin-based superabsorbent

polymer through molecular simulations. The study’s goals are defined below:

1. To crosslink pectin with other chemicals: calcium chloride (CaCl₂), calcium sulfate

(CaSO₄), and polyacrylamide (C3H5NO)n to form new hydrophilic compounds;

2. Identify the best crosslinker;

3. Measure its water absorbency through molecular simulation.

Hypotheses

This research study is anchored with three sets of hypotheses corresponding to the agents

that will be used to cross-link with pectin.

a.)

Hₐ: Pectin-based Superabsorbent Polymer cross-linked by CaCl₂ will score the best in water

absorbency.

Hₒ: Pectin-based Superabsorbent Polymer cross-linked by CaCl₂ will score the worst in water

absorbency.

b.)

Hₐ: Pectin-based Superabsorbent Polymer cross-linked by CaSO₄ will score the best in water

absorbency.

Hₒ: Pectin-based Superabsorbent Polymer cross-linked by CaSO₄ will score the worst in water

absorbency.
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c.)

Hₐ: Pectin-based Superabsorbent Polymer cross-linked by Polyacrylamide will score the best in

water absorbency.

Hₒ: Pectin-based Superabsorbent Polymer cross-linked by Polyacrylamide will score the worst in

water absorbency.

Significance of the Study

This study aims to develop a new compound that can show the best water absorbency.

Having chemicals to cross-link with can help the researcher to make variations and modify each

component. Furthermore, it can contribute to the pre-existing superabsorbent polymer and

discover new hydrophilic compounds as its main ingredient.

This study will also aid in the advancement of research in relation to In silico methods

applied to materials science. Thus, presenting new agents of SAP in combatting drought. Lastly,

this study aims to benefit future researchers in creating much more effective SAPs.

Scope and Limitation

This research study’s main focus is to identify which among the chemicals can be the

best cross-linker to a pectin-based superabsorbent polymer. Other factors such as toxicity and

biodegradability will not be tested in the investigation. This study has no product and the

entirety of experimentation will be done through computer.

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Methods

a. Research Design

The researcher will have two setups, experimental and control setup, cross-links of pectin

to CaCl₂, CaSO₄, polyacrylamide will serve as the experimental setup, commercially available

SAP compound (sodium polyacrylate) for positive control and Pectin-based SAP without any

crosslinkers for negative control.

b. Materials and Preparation

Installation of LAMMPS, MGLTools, PyMol, PACKMOL and Montemplate at any

Windows, Mac, or Linux computer/ laptop. Websites such as PubChem and SwissADME will

also be used in the study.

c. Flowchart
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d. Procedures and Experiment

The researcher will prepare the molecules of Pectin, CaCl₂, CaSO₄, and Polyacrylamide

by removing water H₂O molecules and adding polar hydrogen. Molecules of the said chemicals

can be accumulated through PubChem or SwissADME. Next is to decide what model to use:

there are two models to choose from when performing classical molecular simulations: atomistic

or coarse grained. Atomistic models are used for understanding the local, monomer-lever

(re)arrangements and interactions within an ordered or disordered polymer system. Another

example where atomistic simulations are useful is in studying gas/small molecule

solubility/absorption/diffusion within pores of a polymer membrane (Gartner, 2019). On the

other hand, coarse-grained models are used to predict structure for polymeric systems at a broad

range of conditions or design parameters.

Under atomistic model, finding the right force field may help to identify SAP’s physical
properties (melting temperature, density, cohesive energy, etc.)

Equation 1. Ri are the coordinates of all the atoms in the system, kjl and lj0 are the bond length
constant and equilibrium length of bond j, kjθ and θj0 are the bond angle constant and
equilibrium angle of bond angle j, kjϕ is the dihedral angle constant of dihedral angle j, qi is the
charge on atom i, rij is the distance between atoms i and j, εij is the strength of dispersion
interactions between atoms i and j, and σij is the contact distance between atoms i and j.
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For CG models, each “bead” in a CG model represents a portion of the polymer chains.
The former (more “fine-grained”) models are usually developed/parametrized to represent
specific polymer chemistries, while the latter (more “coarse-grained”) are usually generic and
provide universal properties (e.g., scaling laws relating Rg to molecular weight) for large family
of polymers.

Performing simulation through Molecular Dynamics (MD) will be done through

LAMMPS. After the construction of the simulation domain and constituent molecules,
equilibration must be performed to remove structural artifacts of the system initialization. If the
above basic “brute-force” equilibration at the desired thermodynamic state is not sufficient to
achieve an equilibrated system, then by manipulating the system temperature or pressure in a so-
called “annealing” procedure, one can help the system traverse the free energy landscape more
efficiently. After that is to ensure uncorrelated data points by calculating the time autocorrelation
function of a property of interest.

System analyzation and quantification effort is an essential component after the model
and simulation of setups has been done. In addition, Flory-Huggin's interaction parameter in the
original theory is dimensionless, temperature-dependent, and concentration-independent. The
Thermodynamics and the Flory–Huggins χ will support the study by its ability to measure
thermodynamic properties of polymers such as swelling equilibria of a compound, given the
formula of:
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Equation 2. The temperature dependence of the interaction

Equation 3. For many polymer solutions, χ increases noticeably with polymer concentration

(concentration independence)

Equation 4. It can also be approximated by a power series

Finally, the use of analysis software packages will help the researcher to come up with a

conclusion.

Risk and Safety

Although the study does not require physical experiments, there are still some noteworthy

precautions a researcher must follow. The teacher must assist the student in performing the

experiment safely and observance of screen time is a must. An excessive amount of time spent

on a computer may lead to health problems such as visual, poor sleeping and eating habits.

Data Analysis

The researcher will use One-way ANOVA (Analysis of Variance) to determine the
significant difference between the three sample means.

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