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Chemistry is the study of matter and their composition, structure, properties, behavior and the changes they undergo during a reaction with other compounds. It is an extremely important discipline in science as it provides understanding to the matters we see and the interactions that created everything. For biology, it is one the cornerstone of the study as all lives are made of matters, and it is vital to study their reactions and characteristics.
Chemistry is the study of matter and their composition, structure, properties, behavior and the changes they undergo during a reaction with other compounds. It is an extremely important discipline in science as it provides understanding to the matters we see and the interactions that created everything. For biology, it is one the cornerstone of the study as all lives are made of matters, and it is vital to study their reactions and characteristics.
Element, compounds and mixture
Element, compounds and mixture
Compounds Substance formed when two or more chemical elements are chemically bonded together
Elements. Chemically the simplest substances and hence cannot be broken down using chemical reactions
Mixture Substances that are physically mixed together, but not chemically bonded together.
Atomic theory
Atomic theory
Atomic theory suggests that all matter are composed of discrete units that still carry their distinctive constituent element properties. These discrete units are known as atoms. They are the most basic units that made the world. An atom is understood defined to be chemically indivisible, although the so-called "uncuttable atom" was actually a collection of various subatomic particles (i.e. electrons, protons and neutrons). However, the study of such subatomic particle belongs to the field of particle physics.
Atomic structure
Atomic structure
Current understanding of an atom is depicted with the negatively charged electrons orbiting around the nucleus, which consist of protons (positively charged) and neutrons(neutral). The negatively charged electrons orbits the positively charged nucleus in its specific electron shell. In a free element, the number of proton is equal to the number of electron, a free element is neutral in charge as a result. The number of neutron is also equal to the number of proton. Therefore, the number between proton, electron and neutron is all equal for a free element.
Periodic table and Elements
Periodic table and Elements
From the above understanding of atomic structure, each elements is a distinct chemical species that has the same proton number (Atomic number). There is 118 element identified, with 94 of them naturally occuring and the remaining 24 being artificially synthesized. Each element has a distinct atomic number, mass number and name. Each elements name also has a chemical symbol, which can be understood as the abbreviation of its name (eg. Mg is Magnesium) although there are multiple exceptions (eg, Na is sodium).
Elements are arranged in a table called the periodic table, with rows known as period and columns know as groups. The idea of arranging elements first came in the 18th century when scientist notice there is similarity in chemical properties. In the late 19th century, Dmitri Mendeleev arrange all the known elements at that time in table form and predicted undiscovered elements. Later these predicted elements were discovered, proving his theory in arranging elements in a table is correct.
In the modern day periodic table, elements is arranged into columns (groups) of 8, except for transition metal, lanthanide and actinide. These exceptional does not have groups to them, but period is still applied to them. The groups actually reflects the outermost shell electron of that element. For example, for chlorine (Atomic # 17) belongs to group 7, which means it only has 7 electrons on its outermost shell.
The horizontal row is the period, which indicates the number of electron shell the element possess. Note that as the number of electron shell increases, the atomic radius also increases, meaning the electrostatic attraction between the nucleus to the outer electron shell will decrease. This means electron are easier to be lost at higher electron shells than in lower ones. Different electron shell means the different energy level that the electron posses.
Electron arrangement
Electron arrangement
With the understanding of the periodic table, we can have a better understanding of the electron arrangement of each element. There is actually a maximum amount of electron that each shell can hold, which can be expressed with the equation 2n2 where n is the number of shells.
As mentioned in the above section, elements are arranged in groups of 8, where each group member has the same number of outermost shell electron. To understand the electron arrangement of an element, the number of electron must first be deduced. If it is a free element, the number of electron is same as proton( atomic number). Then the number of shell can be deduced from the period it belongs to. The outermost shell electron number can also be deduced from the group number the element belongs to. Lastly, deduce the electron arrangement by the maximum number of electron for each shell.
Take sodium (Na) atomic (number 19) as example, it has 11 electrons as a free element in total. Knowing that it is period 3 group 1, which means it has 3 electron shell and 1 outermost electron. From this, we know that the first electron shell will take up 2 electrons, the second shell will take up another 8 electrons. Lastly, the third shell will only have one electron. This completely satisfied the original perception of the element. Therefore, the electron arrangement of Na is 2,8,1.
Chemical bonds
Chemical bonds
Chemical bonds refer to how discrete atoms are joined together to form compounds. This can be achieved by adding or reducing the numbers of Electrons (ionic bond), sharing electrons (covalent bond) or having a sea of electrons that attratracts the nucleus(metallic bond). Only ionic and covalent bonds will be discussed below.
Duplet and octet rule
Duplet and octet rule
Duplet and octet is a rule of thumb, stating an atom reaches stability once it has either 2 outermost shell electron (only for Period 1 elements eg.H, He) or 8 outermost shell electron (for period 2 and above). To reach stability, atoms may lose excess electrons, gain deficit electron or even share electron to satisfy the duplet/octet rule for it to reach stability. The ease of carrying out these changes to reach the stability is directly proportional to the reactivity of the element.This change in the original electron arrangement is what leads to chemical bonding, namely ionic bond,covalent bond and metallic bond. Noble gases(group 8) are referred as noble as they are chemically inert (very unreactive), since their outermost shell has reached octet (8 electron)already.
Covalent bonds
Covalent bonds
Overview
Overview
Covalent bond refers to the sharing of valence electron on its outermost shell for both atoms to fulfill the octet rule in order to reach stability. The sharing of electron is a mutual sharing, which means if atom A shares an electron with atom B, both A and B will ‘posses’ the electron. Covalent bond is usually found in organic chemistry, between non-metal and non-metal compounds. It is also possible that 2 atoms of the same elements to bond(the image below shows 2 Cl bonded together, creating a Cl2). However, there is some “grey area” for the statement ‘non metal only’, as metal are sometimes found to covalently bond with non-metal too, such as the Haem group, although it is rare. In covalently bonded pair, the pair of electrons shared is known as the bond pair while the non-bonded one are known as lone pair.
Let’s take H2O as an example. There O is the central atom with 6 outermost shell electron, which requires 2 additional electron for it to fulfill the octet rule. The 2 H atoms, on the other hand, only has 1 electron on its outermost shell, which is lacking 1 electron to fulfill the duplet rule. Therefore, the central O atom shares 2 of its electron with the 2 hydrogen atom, one electron per hydrogen atom. The two O-H bond shares electrons together, which pulls the atoms together.
Notice the 2 bond pair is represented by line while the 2 remaining lone pairs is presented. This is called Lewis structure.
Let’s look at another example, Ammonium (NH4+) is an inorganic compound formed by the reaction of NH3 + H+ ⇌ NH4+
N (Atomic number 7) has 5 outermost shell electron, which means it is lacking 3 electron to fulfill octet rule. The 3 H atoms, on the other hand, only has 1 electron on its outermost shell, which is lacking 1 electron to fulfill the duplet rule. So it shares 3 electron with the 3 Hydrogen atom (one electron per hydrogen), forming NH3. Note that there is a lone pair left for the NH3 , which is donated to H+ , which lacks 2 electron. This donation of electron is still regarded as covalent bond, known as dative covalent bond. Therefore, the NH4+ is formed carries a positive charge due to the H+ .
Inorganic and Organic
Inorganic and Organic
Chemistry can be distinguished into 2 fields according to the elements involved. Organic chemistry, also known as carbon chemistry, refers to the chemistry revolves around hydrocarbons (compounds containing Carbon and hydrogen). Other elements, such as oxygen and nitrogen etc, may also be found in organic compounds. Even compounds may contain carbon or Hydrogen, as long as they do not have C-H bond, they are not classified as organic compound. Carbon is extremely important for chemistry as it has 4 available electron to form covalent bond, allowing for extensive covalent bond formation with single, double or even triple bond. This versatility gives carbon to form extremely complex compound. With that said, covalent bond can still be found in both inorganic and organic compound.
For inorganic compounds, covalent compound is more likely to be found in simple molecules, such as H2O, CO2 . These molecules has covalent bond that join all its constituent atoms. However, a lot of inorganic compounds are formed by ionic bond, which will be discussed in the next section.
For organic compounds, covalent bond is the predominant bond found in all organic compounds (such as CH4), as all C-H bonds are covalent bonds. With the ability to form double or even triple bond with most non-metal elements, the possibilities of forming different compounds is nearly endless, which also allows complex compounds like nucleic acids and amino acids to be formed. All 4 major biomolecules (carbohydrates, lipids, proteins and nucleic acids) are made of manly non-metals and covalent bond is the predominant bond in all these molecules. Covalent bond also allows the formation of polymer either by addition or condensation, which is crucial in forming the biomolecules.
Ionic bond
Ionic bond
The ionic bond refers to the non-directional electrostatic attraction between 2 oppositely charged ions. It is the primary interaction occurring in ionic compounds. An ionic bond forms by the transfer of one or more than one electron (cation, positive ion) to another (anion, negative ion). The atoms become ions in order to reach the octet rule, which stabilize the atom. The octet rule is reached by either losing (lacking electrons) or gaining electrons (too much electron), so it became a positive ion (cation) or negative ion (anion) respectively.
Note that electrons is negatively charged.
In a typical case, ionic bond mostly exhibits between a metal and nonmetal (including polyatomic ions, which may consist some metal as its constituent species). The sample below demonstrates how Sodium (Na) is bonded to the Fluorine, creating sodium Fluoride (NaF). Na has 11 electron (atomic number 11) and belongs to group 1, therefore, its electron configuration is 2,8,1. As it has only has one outermost electron, it has one extra electron than octet rule. The easiest way for it to reach octet is to lose one electron, thus creating Na+ cation. This electron is then taken up by F atom, which is group 7 (lacking 1 electron), allowing it to reach octet too. This also creates an fluoride anion (F -). Since the Na+ and a F - are in opposite charge, an electrostatic attraction is created between the 2 ion, which is the ionic bond. The animation below will demonstrate the ionic bond form between NaF.
Different charges of ions can be formed by gaining or losing more than 1 electron, thus creating the creating different charge (eg. Fe2+ ,Fe3+). Ions may also be polyatomic (both cation and anion), such as NO3- and SO42-. Below is a table shows some of the common ions and its respective charges.
For metals in group 1,2 and 3, the number of positive charges on an ion is equal to its group number. E.g. Na belongs to Group 1, thus its cation exist as Na+. Mg belongs to Group 2, so its charge is 2+, forming Mg2+.
For non-metals in Group 5, 6, and 7, the negative charges on an ion is usually equal to (8- group #). Eg. Cl belongs to Group 7, so it’s anion is Cl- . O belongs to group 6, which is lacking 2 electron from octet, so it’s anion exist as O2-.
Note that ionic bond is not only limited 2 ion, the ratio between the cation and anion is based on the charge of both ions. The net charge of the entire ionic compound must be neutral, therefore the ratio between the 2 ion should allow the charge to balance each other.
Take NaCl as an example. NaCl contain sodium ion and chloride as its constituent chemical species. Notice the ratio between Na+ and Cl- is 1:1, because the charge ratio between Na+and
Cl- is 1+:1-.
Let’s take Al2O3 as another example. The constituent chemical species of Al2O3 is Al3+ and O2- , therefore, it’s charge ratio is 3+ : 2-. To equalize the charge of the 2 oppositely charged ions, the 2 Al3+ is needed to equalize 3 O2- , thus the charge is equalize (6+ : 6-)
Inorganic Chemistry
Inorganic Chemistry
Acid, Bases and pH
Acid, Bases and pH
pH is the scale that ranges from 0 to 14 that measures how acidic (<7) or how basic (>7) the solution is. Acidic and basic solution is defined by the concentration of H+ ion that is ionized. The higher the concentration of H+, the lower pH it is (acidic) and vice versa. The equation of pH is
where the (ɑH+) is the concentration of the H+ ions.
Acid are compounds that can ionize H+ ions from its parent compound, in which the hydrogen atom is previously covalently bonded to the parenting acidic compound. For example, Hydrochloric acid(HCl) is a common acid. When it is dissolved in water, the H ions from the HCl molecule is ionized out ,leaving the Cl- ion. Since H+ ion concentration is higher than the OH- ion concentration.
Base, on the other hand, refers to any substance that can be used neutralize with the acid to form a salt and water. Base can either contain OH- ions as it constituent chemical species (eg. NaOH) that can be dissociated, OH- ions that can be formed by reacting (K2O + H2O → 2 KOH) or can directly react with acid to form salt and water. A soluble base is known as alkali, such as NaOH, KOH and NH3. The higher the OH- ions concentration is, the higher the pH (more alkaline) is.
Therefore, the presence of water is crucial to both acid and base for it to exhibit its acidic or basic properties, as water is needed to ionize or dissociate the respective H+ and OH- ions. Without water, these acids or bases are just solid crystals that is neutral in pH, but once water is added, their acidic or alkaline properties can be observed using pH indicator.
When a base is mixed with acid, neutralization occurs. Salt and water are the products of this reaction, with heat given out as by product (exothermic reaction).
General equation: Acid + Base ⇾ salt+ water.
Eg.1 Hydrochloric acid (HCl) is mixed against Sodium Hydroxide (NaOH)
HCl(aq) + NaOH(aq) → NaCl(aq) + H2O(l) + heat
Noticed how all the substances used in the reaction is balanced in their number (eg. 1 Na is input, and 1 Na is given out as product)
Eg.2 Sulphuric acid (H2SO4) is mixed with Magnesium Oxide (MgO)
MgO(s) + H2SO4(aq)→ MgSO4 (aq)+ H2O(l)
Redox
Redox
Redox is the abbreviation for Reduction-Oxidation reaction, which can occur to both inorganic and organic compounds. This following diagram explains how redox reactions work. Both inorganic and organic compounds can undergo redox reaction.
The reactant 1 (oxidizing agent that oxidizes the opposite reactant) will undergo reduction to give product 1, while the reactant 2 (reducing agent that will reduce the opposite reactant) will undergo oxidation.
Redox reaction is usually explain in terms of gaining or losing of the following 3 substances : hydrogen, oxygen or electron. The following table summarizes all the redox reactions in terms of the 3 substances.
An example for explaining redox by [O] is burning Mg in air, oxidizing to form MgO
Mg+O2 →2MgO
In this reaction, Mg is being oxidized (gaining a [O] to it), where the O2 molecule is being reduced as the diatomic oxygen are being stripped of from each other (losing an [O] for the other oxygen atom). Thus, the reactant (Mg) that oxidized actually makes the other reactant (O2 ) to reduce, so it is called reducing agent, and vice versa.
Take the formation of water from hydrogen (H2) and oxygen (O2)
2H2+O2 → 2H2O
In this reaction, O gains a hydrogen, which means it is reduced by the H2 . at the meantime, H2 gains a oxygen, so it is oxidized. In this case, the O is oxidizing agent while the H is the reducing agent.
The displacement reaction between Mg and CuSO4 is redox reaction in electrons. To be expressed as ionic equation, Mg (s)+ Cu2+ (aq)→ Mg2+ (aq)+ Cu(s).
In this reaction, 2 electron is transferred from the Mg (lossed) to the Cu2+(gained), thus the Mg is oxidised and the Cu is reduced.
Organic Chemistry
Organic Chemistry
Common functional groups
Common functional groups
Functional groups are the group of specially characterized groups of chemical covalently bonded to the remaining of the molecule that gives the chemical a certain property. The following table shows some common functional groups.
Key: R is the hydrocarbon chain.
Properties of some common functional groups
Properties of some common functional groups
Polymers
Polymers
Polymer is a macromolecule composed of multiple repeating units that is bonded together by covalent bond. Before polymerizing into a polymer, the repeating units are known as monomers. A lot of crucial biomolecule are actually polymers, such as DNA, RNA, carbohydrates, and protein. These biomolecules are made from or synthesized by the organism itself, and allows various biochemical functions to be executed. Polymers is mainly divided into 2 categories: Addition and Condensation polymers.
Additional polymer
Additional polymer
Additional polymer simply links up all its monomer without co-generating other by products. These polymer generally requires double bond (alkene) or even triple bond (alkyne) to open up their bonds to bond with another monomer. In additional polymer, all constituent monomers are the same.
Let’s take the addition polymerization of ethene as an example.
Condensation polymer and hydrolysis
Condensation polymer and hydrolysis
It is formed through a condensation reaction, where molecules join together by losing small molecules as byproducts such as water or methanol. All condensation polymers are made from 2 different constituent monomers. Polyamides and polyester are common condensation polymers. However this reaction is reversible, adding water will result in the separation of the molecule, known as hydrolysis.
Such a polyamide is composed of carboxylic acid and Protein (composed of amino acid as monomers, which has carboxylic acid on one side and amine group on the other side) are linked together by amide linkage, which is a condensation polymer. The amine group NH2 (N-terminal) is bonded to the Carboxylic acid COOH (C-terminal) with the formation of 1 water molecule as by-product.
The final product is formation of amide bond, which links the 2 monomers together. The by-product of this reaction is a water molecule
Lipids, on the other hand, is formed by ester bond. An ester is formed by an alcohol and a carboxylic acid condensed together. Triglycerides is made of glycerol and 3 fatty acid.
Polarity of molecules and Intermolecular molecular forces
Polarity of molecules and Intermolecular molecular forces
Intermolecular force
Intermolecular force
Intermolecular force (abbreviated as IMF) are the weak electrostatic attractions that exist between molecules. It is the primary factor that determines the melting and boiling point of a chemical species. Usually, the more intermolecular forces exist between molecules, the higher the melting and boiling point will bec higher, as more energy is needed to break these intermolecular forces.
IMF is usually categorized into a few different types of intermolecular forces, namely Van der Waals’ force and hydrogen bond.
Van der Waals force
Van der Waals force
Van der Waals’ force (abbreviated as VDW) is the electrostatic intermolecular attractive force that exist among all molecules, no matter the molecules is polar or nonpolar.
For a polar molecule, to explain the formation of VDW, a partial positive charge (ẟ+) is carried by one side of the molecule and a small negative charge (ẟ-) is carried by the other end of the molecule. This small partial charge is formed due to the polarity of the molecule.
Take Hydrogen Chloride (HCl) as an example, it is a polar molecule, as the Cl is highly electronegative. Therefore, the Cl side of HCl is slightly more negative than the H side, creating a partial negative charge and thus forms the VDW force.
Even water (H2O) molecule is polar even though there’s is 2 polar O-H bond that would seem to counter each other. However the shape of the molecule makes the molecule polar. The 2 polar O-H bond is repelled by the lone pair electron, making the molecule polar as a whole, thus water is a great solvent.
For a nonpolar molecule, the partial charge can be formed by the uneven distribution of electrons at any given moment, thus one side of the molecule may have more electron than the other. However, this partial charge is not permanent, where it will continue to arise and disappear all the time. This charge allows for the electrostatic attraction to pull the molecules together. This is why VDW for nonpolar molecules is very weak, so these nonpolar compounds usually has a low boiling and melting point.
For instance, Cl2 is a diatomic molecule composed of 2 chlorine atoms, which means it is a nonpolar molecule as the electronegativity of both Cl is identical. Therefore, VDW is the primary intermolecular force, but as mentioned, there is no permanent dipole to Cl2 as it is non-polar. This makes the non-permanent partial charge very weak, so it has low VDW. As a result, little energy is needed to overcome the VDW to break the molecules apart, which is shown by the low melting point (−101.5 °C) and boiling point (−34.04 °C).
Hydrogen Bond
Hydrogen Bond
A hydrogen bond is an electrostatic attraction between a Hydrogen (H) which is bound to a highly electronegative atom (eg. N,O,F), and another adjacent atom bearing a lone pair of electrons. It can be found both organically (eg. Water) and inorganically (eg. ethanoic acid). It is also the reason that water is such an excellent solvent as the hydrogen bond allow it to attract other electrically charged molecules, such as ionic compounds.
The formation of a hydrogen bond requires at least
- One molecule must carry an H atom bonded to the highly negative electronegative atom (eg. N,O,F)
- The other molecule must provide a lone pair electrons from N, O or F.
The hydrogen bond is formed when a hydrogen atom is directly bonded to a highly electronegative atom (eg. N,O,F), a highly polar bond forms. The bond pair of electron is drawn closer to the highly electronegative atom due to the large difference in electronegativity. Thus, the H atom carries a partial positive charge. On the other, the exposed lone pair from N, O or F is highly electronegative. Thus an electrostatic attraction between the partial positive charge (from the H atom) and the lone pair electron is formed, and is known as the hydrogen bond.
Let's take water as an example. There are 2 lone pair electrons on the Oxygen atom in H2O, and 2 hydrogen attached to the oxygen atom. This means that each H2O can form 2 hydrogen bond on average. Notice how one H2O molecule is hydrogen-bonded to more than 1 H2O molecule, thus creating a network of H2O molecules bonded by hydrogen bond.
It is an extremely important intermolecular interaction for biochemistry, as it is the primary intermolecular interaction that forms and give specific conformation to DNA molecules and protein.
Hydrogen bond allows the 2 strands of DNA to maintain a double helix and and allow for the contemporary base pairing (A pairs with T, C pairs with G).
For protein, hydrogen bond is the key factor in contributing to the secondary structure of protein, such as α-helixes and β-sheets. Therefore, hydrogen bond is extremely important in biochemistry.
Molecular shapes
Molecular shapes
The molecular shape refers to the 3D arrangement of the atoms that constitute a molecule. The VSEPR theory can help explain the molecular shape. By this theory, molecular shapes is dictated mainly by the electrons repelling each other and trying to get as far apart as possible. This repulsion of electrons is not exclusive to all bond pairs and lone pairs, but to all bonds, including double or triple bonds. The repelling effect of the different electron is as follow:
lone pair- lone pair repulsion > lone pair-bond pair repulsion>bond pair-bond pair repulsion
The image belows show you some of the most common molecular shapes.
Take NH3 as an example, the N atom (atomic number 7) has 5 outermost with 3 N-H bond pairs and 1 lone pair. For the all 4 electron pairs to repel from each other in a furthest possible manner, they should take up a tetrahedral arrangement. However, as the shape of the molecule depends only in the position of bonded atoms, the NH3 will take up trigonal pyramidal shape. The lone pair at the top will also exert a greater repulsion on the bond pairs, thus the 3 bond pairs is pushed downwards.
Structure of substances
Structure of substances
It refers to the how the constituent chemical species in a substance is arranged.
Molecular structures
Molecular structures
This structure consist of discrete molecules bonded by strong covalent bonds, while the neighboring molecules is attracted by intermolecular force.
Simple molecular structure (SMS)
Simple molecular structure (SMS)
Most non-metal and covalent compounds are composed of simple and discrete molecules.
Eg. CO2, NH3 ,O2 , N2
Giant structure
Giant structure
Giant Ionic structure (GIS)
Giant Ionic structure (GIS)
All ionic compounds under room condition exist as solids that are regularly packed together to form a continuous 3D giant ionic structure. This structure allows the ions to be be surrounded by ions of the opposite charge. They are all crystalline in solid state due to this structure.
Eg. NaCl
Giant covalent structure (GCS)
Giant covalent structure (GCS)
In some non-metal elements and compounds, atoms are joined by strong covalent bond to form a giant covalent structure. In this structure, the covalent bond is extended throughout the whole structure with no discrete molecule.
Eg. Diamond
It is only composed of carbon. The extensive covalent bond results in a extremely strong structure, which makes diamond the hardest substance on earth and the has very high melting point.
Eg. Graphites
Graphites is also exclusively composed of carbon, but is arranged into flat, parallel layers of carbon (bonded by covalent bonds). Only weak Van der Waals’ force holds the layers together, making slippery in touch. It also has a extremely high melting point (3730°C)
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