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The Name’s Bond ... Ionic Bond.

This is the first in my short series of the three main types of bond - ionic, metallic and covalent. In this, you’ll learn about the properties of the compounds, which atoms they’re found between and how the bonds are formed. Enjoy!

When electrons are transferred from a metal to a non-metal, an ionic compound is formed. Metals usually lose electrons and non-metals usually gain them to get to a noble gas configuration. Transition metals do not always achieve this.

Charged particles that have either lost or gained electrons are called ions and are no longer neutral - metal atoms lose electrons to become positive ions (cations) whereas non-metals gain electrons to become negative ions (anions).

The formation of these ions is usually shown using electron configurations. Make sure you know that the transfer of electrons is not the bond but how the ions are formed. 

An ionic bond is the electrostatic attraction between oppositely charged ions.

You need to know how to explain how atoms react with other atoms and for this the electron configurations are needed. You can use dot and cross diagrams for this. 

Ionic solids hold ions in 3D structures called ionic lattices. A lattice is a repeating 3D pattern in a crystalline solid. For example, NaCl has a 6:6 arrangement - each Na+ ion is surrounded by 6 Cl- and vice versa. 

Ionic solids have many strong electrostatic attractions between their ions. The crystalline shape can be decrepitated (cracked) on heating. Ionic Lattices have high melting and boiling points since they need more energy to break because atoms are held together by lots of strong electrostatic attractions between positive and negative ions. The boiling point of an ionic compound depends on the size of the atomic radius and the charge of the ion. The smaller the ion and the higher the charge, the stronger attraction.

Look at this diagram. It shows how atomic radius decreases across a period regularly. This is not the case with the ions. Positive ions are usually smaller than the atoms they came from because metal atoms lose electrons meaning the nuclear charge increases which draws the electrons closer to the nucleus. For negative ions, they become larger because repulsion between electrons moves them further away - nuclear charge also decreases as more electrons to the same number of protons.

Ionic substances can conduct electricity through the movement of charged particles when molten or dissolved (aqueous). This is because when they are like this, electrons are free to move and carry a charge. Ionic solids cannot conduct electricity.

Ionic compounds are usually soluble in water. This is because the polar water molecules cluster around ions which have broken off the lattice and so separate them from each other. Some substances like aluminium oxide have too strong electrostatic attractions so water cannot break up the lattice - it is insoluble in water.

Molecular ions such as sulfate, nitrate, ammonium or carbonate can exist within ionic compounds. These compounds may have covalent bonds within the ions but overall they are ionic and exhibit thee properties described above.

SUMMARY

When electrons are transferred from a metal to a non-metal, an ionic compound is formed.

Charged particles that have either lost or gained electrons are called ions and are no longer neutral - metal atoms lose electrons to become positive ions (cations) whereas non-metals gain electrons to become negative ions (anions).

The formation of these ions is usually shown using electron configurations. The transfer of electrons is not the bond but how the ions are formed.

An ionic bond is the electrostatic attraction between oppositely charged ions.

Ionic solids hold ions in 3D structures called ionic lattices. A lattice is a repeating 3D pattern in a crystalline solid.

Ionic solids have many strong electrostatic attractions between their ions. The crystalline shape can be decrepitated (cracked) on heating. 

Ionic Lattices have high melting and boiling points since they need more energy to break because atoms are held together by lots of strong electrostatic attractions between positive and negative ions.

The boiling point of an ionic compound depends on the size of the atomic radius and the charge of the ion. The smaller the ion and the higher the charge, the stronger attraction.

 Positive ions are usually smaller than the atoms they came from because metal atoms lose electrons meaning the nuclear charge increases which draws the electrons closer to the nucleus. Negative ions become larger because repulsion between electrons moves them further away - nuclear charge also decreases as more electrons to the same number of protons.

Ionic substances can conduct electricity through the movement of charged particles when molten or dissolved (aqueous). This is because when they are like this, electrons are free to move and carry a charge. Ionic solids cannot conduct electricity.

Ionic compounds are usually soluble in water because the polar water molecules cluster around ions which have broken off the lattice and so separate them from each other.

 Some substances like aluminium oxide have too strong electrostatic attractions so water cannot break up the lattice - it is insoluble in water.

Molecular ions such as sulfate, nitrate, ammonium or carbonate can exist within ionic compounds. These compounds may have covalent bonds within the ions but overall they are ionic and exhibit thee properties described above.

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Shapes of Molecules

his post is more information than trying to explain something - the truth is, you just need to learn shapes of molecules like you do with anything. I’ve got a physical chemistry mock tomorrow that I’m dreading since I’ve done zero revision. The fact that I run a study blog yet don’t revise myself is odd, but what else can I do? Oh, wait … revise. So here it is, my last minute revision for myself and you too - I present, shapes of molecules!

VSEPR stands for valence shell electron pair repulsion theory. If you’ve ever seen a moly-mod or a diagram of a molecule in 3D space, you may wonder how they decided it was that shape. Well, VSEPR answers all.

The theory essentially states that electron pairs are arranged to minimise repulsions between themselves - which makes sense, since electrons carry the same charge and therefore try to repel each other. Of course, there are different types of electron pairs, lone and bonding. The strongest repulsions happen between lone pair - lone pair followed by lone pair - bonding pair and finally, bonding pair - bonding pair have the least repulsion. 

Since the repulsion governs the shape of the molecule, to work out a molecule’s shape you must look at dot and cross diagrams or electron configurations to see how a molecule is bonded. There are many methods to do this, but the bottom line is that you must work out how many bonding pairs of electrons and how many lone pairs are involved.

The easiest shape to learn is linear. This has two bonding pairs and no lone pairs at an angle of 180 degrees, since that is the furthest the two can get away from each other. Examples of linear molecules include carbon dioxide and beryllium chloride.

Next up is trigonal planar. This has three bonding pairs and no lone pairs, each at the angle of 120 degrees. Trigonal means three and planar means on one plane, this should help you in identifying the molecules since after a fourth pair of electrons, the shape becomes 3D. Examples of trigonal planar molecules include boron trifluoride and sulfur trioxide.

What if you were to have two bonding pairs and two lone pairs? Well, then you’d have a bent molecule. Water is a good example of a bent molecule. Since it has two lone pairs that repel the other two bonding pairs more than they repel each other, the bond angle is 104.5. I’d be careful though, as in many textbooks it shows a bent molecule to have one lone pair and a different bond angle.

Another variation of the bent molecule I’ve seen is the one with two bonding pairs and one lone pair. It is deemed as bent with a bond angle of 109 or sometimes less than 120 degrees.

Tetrahedral molecules have four bonding pairs and no lone pairs. The bond angle is 109.5 degrees. Examples of this include the ammonium ion, methane and the phosphate ion. A good thing to note here is how these molecules are drawn. To demonstrate the 3D shape, where the molecule moves onto a plane, it is represented with a dashed line and triangular line along with a regular straight line. 

Trigonal pyramidal, sometimes just called pyramidal, is where there are three bonding pairs and a lone pair. Bond angles are roughly 107 degrees due to the repulsion from the lone pairs. An example of a trigonal pyramidal molecule is ammonia, which has a lone pair on the nitrogen.

Having five bonding pairs gives a trigonal bipyramidal structure. I guess the three bonding pairs on the trigonal plane accounts for that part of the name, where the rest comes from the position of the remaining two. These molecules have no lone pairs and have a bond angle of 90 degrees between the vertical elements and 120 degrees around the plane. Diagrams below are much clearer than my description! Examples of this include phosphorus pentachloride.

Six bonding pairs is an octahedral structure. I know this is confusing because octahedral should mean 8 but it’s one of those things we get over, like the fact sulfur isn’t spelt with a ph anymore. It’s actually to do with connecting the planes to form an octahedral shape.There are no lone pairs and each bond angle is a nice 90 degrees. Common examples include sulfur hexafluoride.

Square planar shapes occur when there are six bonding pairs and two lone pairs. All bond angles are 90 degrees! They take up this shape to minimise repulsions between electrons - examples include xenon tetrafluoride.

The final one to know is T-shape. This has three bonding pairs and two lone pairs. These molecules have bond angles of (less than) 90 degrees, usually a halogen trifluoride like chlorine trifluoride.

There are plenty more variations and things you could know about molecular geometry, but the truth is, there won’t be an extensive section on it. It’s a small part of a big topic!

I’m not going to do a summary today since I’d just be repeating the same information (I tried to keep it concise for you guys) so instead I’ll just leave you with, 

Happy studying!

Haloalkanes and Their Angelic Reactions: Part One

Haloalkanes are more commonly referred to as halogenoalkanes. Obviously you’ve already read my post on halogenoalkanes and their properties so there’s no surprise that you’re itching to read what I’ve got to say about these beauties and their reactions! Should we delve in?

There are a few different kinds of reactions you must learn for the A Level exam that involve halogenoalkanes. 

The first is the synthesis of chloroalkanes via the photochemical chlorination of the alkanes. I know it looks scary, but don’t worry, it is simpler than it sounds. It essentially means “forming chloroalkanes through chlorinating an alkane in the presence of sunlight”.

Chlorine will react with methane when UV light is present and will form several kinds of chloroalkanes and fumes of hydrogen chloride gas. Chloromethane was once commonly used as a refridgerant. Depending on how many chlorine molecules there are, there will be different compounds formed:

methane + chlorine -> chloromethane + hydrogen chloride

CH4 + Cl2 -> CH3Cl + HCl

or

methane + chlorine -> trichloromethane + hydrogen chloride

CH4 + 3Cl2 -> CHCl3 + 3HCl

When undergone in real life, mixtures of halogenoalkanes are produced with some long chain alkanes which can be separated out with fractional distillation. 

To understand what happens in an overall chemical reaction, chemists use mechanisms. These basically show the step-by-step process that is usually shown by a simple symbol equation that summarises everything.

The chlorination of methane is something you must learn the mechanism for. It’s pretty easy but involves a lot of steps and must be revised periodically to remember them.

The actual reaction is a substitution reaction because one atom or group is replaced by another. Since the chlorine involved is a free radical, it can also be called a free-radical substitution reaction.

1. Initiation

UV light is essential for the first step in the mechanism. This breaks the Cl-Cl covalent bond so that each chlorine leaves with one electron from the shared pair. Chlorine free radicals, with one unpaired electron in the outer shell, are formed. Free radicals are only formed if a bond splits evenly - each atom getting one of the two electrons. The name given to this is homolytic fission.

2. Propagation

This has two sub-steps

(a) Chlorine free radicals (highly reactive) react with methane to form hydrogen chloride and leave a methyl free radical.

Cl• + CH4 -> HCl + •CH3

(b) This free radical then reacts with another chlorine to form chloromethane and another chlorine free radical. Producing free radicals is a chain reaction which is why it is such a problem in ozone depletion - a little amount can cause a lot of destruction.

•CH3 + Cl2 -> CH3Cl +  •Cl

3. Termination

This step stops the chain reaction. It only happens when two free radicals collide to form a molecule in several ways:

Cl• + Cl• -> Cl2

UV light would just break down the chlorine molecule again, so although this is technically a termination reaction it is not the most efficient.

Cl• +  •CH3 -> CH3Cl

Forming one molecule of methane uses one chlorine and one methyl free radical.

•CH3 +  •CH3 -> C2H6

Ethane can be formed from two methyl free radicals - this is why there are longer chain alkanes in the mixture. 

This whole process is how organic halogenoalkanes are the product of photochemical reactions of halogens with alkanes in UV light - made via free radical substitution mechanisms in chain reaction.

Another reaction you need to know is a nucleophilic substitution reactions. A nucleophile is an electron pair donor or proton acceptor - the name comes from Greek origins (”loves nucleus”) - such as hydroxide ions, cyanide ions or ammonia molecules. Hydroxide and cyanide ions are negative but ammonia is neutral.

Halogenoalkanes have a polar bond because of the difference between the highly electronegative halogen and the carbon atom. The 𝛿+ carbon can go under nucleophilic attack. The mechanism for negatively charged nucleophiles these in general is:

Nu represents the nucleophile. This example is with a bromoalkane. Make sure to include curly arrows that begin at a lone pair or the centre of a bond and end at an atom or centre of bond, and delta (slight) charges.

Lets look at a more specific example:

One nucleophile that can be used is a hydroxide ion, found in either water or sodium hydroxide. In this case, you need to know about aqueous sodium hydroxide or potassium hydroxide and a halogenoalkane. This takes place at room temperature but is slow so is often refluxed (continuously boiled and condensed back into the reaction flask). Reflux apparatus is shown below:

The halogenoalkane is dissolved into ethanol since it is insoluable in water and this solution along with the aqueous hydroxide can mix. The product produced is an alcohol, which is organic.

The general reaction is:

R-CH2X + NaOH -> CH3CH2OH + NaX

Where X represents a halogen.

You must learn the mechanism for this reaction. The lone pair on the hydroxide attacks the carbon atom attached to the halogen and this causes both carbon electrons to move to the halogen which becomes a halide ion.

The reaction of a hydroxide ion can also be classed as a hydrolysis reaction as it breaks down chemical bonds with water or hydroxide ions. The speed of reaction depends on the strength of the bond - a stronger carbon-halogen bond, a slower reaction.

C-I is the most reactive (reactivity increases down group 7) and C-F is therefore the least reactive and strongest.

Part two of this post will cover nucleophilic substitution of cyanide ions and ammonia molecules, as well as elimination reactions.

SUMMARY

You need to know about the synthesis of chloroalkanes via the photochemical chlorination of the alkanes. - “forming chloroalkanes through chlorinating an alkane in the presence of sunlight”.

Chlorine will react with methane when UV light is present and will form several kinds of chloroalkanes and fumes of hydrogen chloride gas. Depending on how many chlorine molecules there are, there will be different compounds formed.

When undergone in real life, mixtures of halogenoalkanes are produced with some long chain alkanes which can be separated out with fractional distillation. 

To understand what happens in an overall chemical reaction, chemists use mechanisms. These basically show the step-by-step process.

The chlorination of methane is something you must learn the mechanism for. The actual reaction is a substitution reaction because one atom or group is replaced by another. 

The first step is initiation - UV light is essential for the first step in the mechanism. This breaks the Cl-Cl covalent bond so that each chlorine leaves with one electron from the shared pair. Chlorine free radicals, with one unpaired electron in the outer shell, are formed. Free radicals are only formed if a bond splits evenly - each atom getting one of the two electrons.

Step two is propagation: (a) Chlorine free radicals (highly reactive) react with methane to form hydrogen chloride and leave a methyl free radical (b) this free radical then reacts with another chlorine to form chloromethane and another chlorine free radical. Producing free radicals is a chain reaction which is why it is such a problem in ozone depletion - a little amount can cause a lot of destruction.

To stop the chain reaction, the final step is termination. It only happens when two free radicals collide to form a molecule in several ways: two chlorine free radicals forming a chlorine molecule, two methyl FRs forming ethane or a chlorine FR and a methyl FR forming chloromethane.

Ethane contributes to the longer chain alkanes in the mixture. 

Another reaction you need to know is a nucleophilic substitution reactions. A nucleophile is an electron pair donor or proton acceptor, such as hydroxide ions, cyanide ions or ammonia molecules. Hydroxide and cyanide ions are negative but ammonia is neutral.

Halogenoalkanes have a polar bond because of the difference between the highly electronegative halogen and the carbon atom. The 𝛿+ carbon can go under nucleophilic attack. 

Nu represents the nucleophile. Make sure to include curly arrows that begin at a lone pair or the centre of a bond and end at an atom or centre of bond, and delta (slight) charges.

One nucleophile that can be used is a hydroxide ion, found in either water or sodium hydroxide. In this case, you need to know about aqueous sodium hydroxide or potassium hydroxide and a halogenoalkane. This takes place at room temperature but is slow so is often refluxed (continuously boiled and condensed back into the reaction flask). The halogenoalkane is dissolved into ethanol since it is insoluable in water and this solution along with the aqueous hydroxide can mix. The product produced is an alcohol, which is organic.

The general reaction is :R-CH2X + NaOH -> CH3CH2OH + NaX where X represents a halogen

The lone pair on the hydroxide attacks the carbon atom attached to the halogen and this causes both carbon electrons to move to the halogen which becomes a halide ion.

The reaction of a hydroxide ion can also be classed as a hydrolysis reaction as it breaks down chemical bonds with water or hydroxide ions. 

The speed of reaction depends on the strength of the bond - a stronger carbon-halogen bond, a slower reaction. C-I is the most reactive (reactivity increases down group 7) and C-F is therefore the least reactive and strongest.

Biochemistry

Update: Pictures are working!

Atoms

There are a few basic chemistry concepts that are essential to understand. For starters, understanding what an atom is and its basic properties.

Atoms are the building block of all matter. They have a positive nucleus, with positive protons, and neutral neutrons. In a large area surrounding the nucleus, is the electron cloud, made of negatively charged electrons.

An atom in its elemental state is always neutral.

When an element has a charge, it is because it has an unequal number of protons an electrons, making it an ion. Sometimes an element’s nucleus has an unequal number of neutrons and protons, making it an isotope. Carbon-14, for example, has 8 neutrons, instead of the 6 that Carbon-12 has. Carbon-14 is also a radioisotope, meaning it emits particles and decays at a rate called a half-life, making it useful for fossil dating. Along with that, radioactive carbon can be used as a tracer. This means it is incorporated in CO2 molecules and used to track metabolic pathways.

The location of the electron affects how the atom will react with other elements. When electrons are in the lowest available energy level, they are in the ground state. When they absorb energy, they move to a higher energy level, entering the excited state. For instance, when chlorophyll absorbs light energy, electrons within it are boosted to higher energy levels. This provides the energy necessary to produce sugar when they return to their ground state level as they release the energy they absorbed.

Bonding

Elements bond when two nuclei are attracted to each other. Energy is released when a bond is formed. All atoms want to either get rid of all their electrons on their outer shell or fill their outer shell with 8 (or in hydrogen’s case, 2) electrons, which makes them stable. There are 3 kinds of bonds, but for biochemistry, Ionic and covalent bonds are what is relevant.

Ionic bonds form ions (hence the name.) They occur when electrons are transferred. The atom that gains electrons becomes a negatively charged anion. The atom that loses electrons becomes a positively charged cation.

Covalent bonds are made when electrons are shared. This occurs when the two atoms have electronegativities that are closer together than in an ionic bond. Electronegativity is the tendency of an atom to pull electrons towards it. These bonds can be polar if the electronegativity is high enough. A polar molecule is a molecule with a partial charge. For example, water is a polar molecule, as oxygen is extremely electronegative, and water is partially electronegative.

Hydrogen Bonding

Hydrogen bonding is a specific kind of intermolecular force that is essential to life. It is what keeps the 2 strands of DNA bonded together, and gives water its unique characteristics. Since oxygen has a partial negative charge, and hydrogen has a partial positive charge, they are naturally drawn to each other.

Hydrophobic vs Hydrophilic

Polar molecules are hydrophilic. This is because they are attracted to the partially charged ends of water. Hydrophilic means they are attracted to water. (Not in that way… sick) NaCl or table salt is hydrophilic. This is why salt dissolves in water.

Non-polar molecules are hydrophobic. This means they are repelled by water. (They’re filthy water haters.) Lipids are hydrophobic, which is why fats and oils do not dissolve in water.

The cell membrane is a phospholipid bilayer, only allowing nonpolar substances to dissolve through it. Large polar molecules have to use specific hydrophilic channels.

Characteristics of Water

Water is a unique molecule, and without its unique properties, life on earth would not exist as it does, or even at all.

Water has a high specific heat: Because hydrogen bonds are so strong, it requires a lot of heat energy to break them. This is why large bodies of water remain the same temperature, and why coastal cities have a consistent temperature because the water absorbs all the heat energy before it can warm up.

Water has a high heat of vaporisation: A large amount of energy is needed for water to vaporise, which is why sweating is such an effective cooling method.

Water has high adhesion properties: Adhesion is when one substance clings to another. Adhesion causes capillary action, which occurs in the xylem of plants, and is used to bring water up from the roots without expending energy.

Water is a universal solvent: Due to its high polarity, water makes an excellent solvent.

Water is extremely cohesive: Molecules of water tend to stick to each other. This is observed in surface tension and allows for small insects to run across the surface of the water. Cohesion is also necessary to bring water up from the roots, by transpirational-pull cohesion tension.

Ice is less dense than water: Instead of freezing all the way through, ice crystallises, leaving large amounts of space, causing ice to float. This is essential for the survival of marine life during the winter, as they can live beneath the ice.

pH

pH is calculated by taking the -log of the chance of finding hydronium (H30+) ions within a certain amount of water. Hydronium is made in rare circumstances, where a hydrogen ion breaks off from a water molecule. Normally, there is a 1 in 10 million chance of there being a hydronium ion. This is the equivalent of 1x10^-7. The -log of this number is 7, the neutral pH.

Any pH below 7 is acidic. Any pH above 7 is basic. Stomach acid has a pH of 2, while bleach has a pH of 11. Human blood has a pH of around 7.4

Most living cells need to have an internal environment with a pH of around 7. Buffers exist to regulate pH by either absorbing excess hydrogen ions or donating missing hydrogen ions. In human blood, the bicarbonate ion (HCO3) is essential.

Macromolecules

There are 4 types of macromolecules: carbohydrates, lipids, proteins, and nucleic acids.

Carbohydrates

Carbohydrates are made of carbon, hydrogen, and oxygen. They supply quick and easy energy. 1 gram of all carbohydrates will release 4 calories of energy. In our diet, they can be found almost everywhere in foods such as rice, pasta, bread, cookies, etc.

There are 3 kinds of carbohydrates: monosaccharides, disaccharides, and polysaccharides.

Monosaccharides

All monosaccharides have a chemical formula of C6H12O6. It is the placement of the carbon, oxygen, and hydrogen that determines its properties. Glucose, fructose, and galactose are all examples. They are isomers, meaning they have the same chemical formula, but a different structure.

Disaccharides

When 2 monosaccharides join together, they create disaccharides. They all have the chemical formula C12H22O11. Dehydration synthesis is the process that creates them. This process releases 1 molecule of water, hence the name. Lactose, maltose, and sucrose are all examples.

Hydrolysis is the exact opposite of dehydration synthesis. It is used during digestion. One molecule of water is used to breakdown polymers into monomers.

Polysaccharides Polysaccharides are long polymers of carbohydrates. Cellulose (plant cell wall), chitin (exoskeleton, fungi cell wall), glycogen (how animals store carbohydrates) and starch (how plants store carbohydrates) are all examples.

Lipids

Lipids include fats, oils, and waxes. Most contain 1 glycerol and 3 fatty acids. Glycerol is alcohol.

Fatty acids are the building blocks of lipids and are hydrocarbon chains with carboxyl groups at the end. There are 2 varieties; saturated and unsaturated. (3 if you count trans-fats when extra hydrogen is added to the fat to make the lipid solid)

Saturated fats are solid at room temperature, and are famously unhealthy as they are linked to heart disease.

Unsaturated fats are liquid at room temperature and are good dietary fats.

Lipids store much more energy than carbohydrates. 1 gram of any lipid will release 9 calories of heat per gram. They can be structural, as in the phospholipids of the cell membrane, or they can be hormones.

Proteins

Proteins are polymers of amino acids linked together by peptide bonds.

Amino acids are identifiable by their carboxyl group, amine group, and variable R, attached to a central carbon atom.

Proteins are complex and perform a vast array of duties, such as growth and repair, being enzymes, membrane channels, and hormones.

1 gram of protein releases 4 calories of heat.

Proteins contain the elements C H O N P S

There are only 20 amino acids coding for the thousands of proteins in the human body.

Protein Structure

There are 4 levels to the structure of a protein.

The primary structure results from the sequence of amino acids making up the polypeptide

The secondary structure results from hydrogen bonding within the molecule. This causes a helical structure

The tertiary structure is an intricate 3-dimensional shape or conformation of a protein and most directly decides the function of the protein. Enzymes denature in high temperatures or in the wrong pH because the tertiary structure is compromised.

The quaternary structure is only found in proteins that have more than 1 polypeptide chain, such as in haemoglobin.

Enzymes

Enzymes are large proteins

Enzymes lower the energy of activation, speeding up the reaction, as it lowers the amount of energy needed to start the reaction.

The chemical an enzyme works on is known as a substrate

Enzymes are specifically designed for specific substrates. For example, lactase only works on lactose. Notice the naming pattern for enzymes and their substrates.

The induced fit model is an explanation for how they work. When the substrate enters the active site, it induces the enzyme to change its shape to fit the substrate.

Enzymes can be reused as they do not degrade during a reaction

Enzymes are assisted by cofactors (minerals) or coenzymes (vitamins)

Prions

Prions are proteins that cause diseases. Mad cow disease is an example. It is a misformed protein able to influence other proteins to fold in the same way.

Nucleic Acids

There are 2 kinds of nucleic acids: RNA and DNA. They are necessary for carrying genetic information.

Nucleic acids are polymers of nucleotides

The nucleotides are the two purines: Adenine and Guanine, and the 3 pyrimidines, Thymine, Uracil, and Cytosine. Uracil is only found in RNA, and thymine is only found in DNA. Adenine connects with thymine/uracil, and guanine connects with cytosine.

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Covalent and Dative Bonds

Covalent and dative (sometimes called co-ordinate) bonds occur between two or more non-metals,  e.g. carbon dioxide, water, methane and even diamond. But what actually are they?

A covalent bond is a chemical bond that involves the sharing of electron pairs between atoms. They are found in molecular elements or compounds such as chlorine or sulfur, but also in macromolecular elements and compounds like SiO2 and graphite. Covalent bonds are also found in molecular ions such as NH4+ and HCO3-.

Single covalent bonds have just one shared pair of electrons. Regularly, each atom provides one unpaired electron (the amount of unpaired electrons is usually equal to the number of covalent bonds which can be made) in the bond. Double covalent bonds have two shared pairs of electrons, represented by a double line between atoms, for example, O=C=O (CO2). Triple covalent bonds can also occur such as those in N ≡ N.

Dot and cross diagrams represent the arrangement of electrons in covalently bonded molecules. A shared pair of electrons is represented by a dot and a cross to show that the electrons come from different atoms.

Unpaired electrons are used to form covalent bonds as previously mentioned. The unpaired electrons in orbitals of one atom can be shared with another unpaired electron in an orbital but sometimes atoms can promote electrons into  unoccupied orbitals in the same energy level to form more bonds. This does not always occur, however, meaning different compounds can be formed - PCl3 and PCl4 are examples of this.

An example where promotion is used is in sulfur hexafluoride (SF6). The regular configuration of sulfur atoms is 1s2 2s2 2p6 3s2 3p4. It promotes, as shown in the diagram (see excited state), two electrons: one from the 3s electrons to the 3d orbital and one from the 3p to the 3d. Therefore there are 6 unpaired electrons for fluorine atoms to join. It has an octahedral structure.

An atom which has a lone pair (a pair of electrons uninvolved in bonding) of electrons can form a coordinate bond with the empty orbital of another atom. It essentially donates an electron into this orbital which when formed, acts the same as a normal covalent bond. A coordinate bond therefore contains a shared pair of electrons that have come from one atom.

When ammonia reacts with a H+ ion, a coordinate bond is formed between the lone pair on the ammonia molecule and the empty 1s sub-shell in the H+ ion. An arrow represents the dative covalent bond (coordinate bond). Charges on the final ion must be showed.

Summary

A covalent bond is a chemical bond that involves the sharing of electron pairs between atoms. They are found in molecular elements or compounds as well as in macromolecular elements and compounds. Also found in molecular ions.

Single covalent bonds have just one shared pair of electrons.  Double covalent bonds have two shared pairs of electrons, represented by a double line between atoms. Triple covalent bonds can also occur.

Dot and cross diagrams represent the arrangement of electrons in covalently bonded molecules. A shared pair of electrons is represented by a dot and a cross to show that the electrons come from different atoms.

Unpaired electrons are used to form covalent bonds - they can be shared with another unpaired electron in an orbital but sometimes atoms can promote electrons into unoccupied orbitals in the same energy level to form more bonds. This does not always occur, however, meaning different compounds can be formed.

An example where promotion is used is in sulfur hexafluoride (SF6). 

An atom which has a lone pair (a pair of electrons uninvolved in bonding) of electrons can form a coordinate bond with the empty orbital of another atom.

 It donates an electron into this orbital which when formed, acts the same as a normal covalent bond. A coordinate bond therefore contains a shared pair of electrons that have come from one atom.

When ammonia reacts with a H+ ion, a coordinate bond is formed between the lone pair on the ammonia molecule and the empty 1s sub-shell in the H+ ion. An arrow represents the dative covalent bond (coordinate bond). Charges on the final ion must be showed.

#Thunderstorms are hitting the UK this week – here’s how thunder and lightning happen and some of the chemistry going on during a storm: https://ift.tt/2XUCKZc https://ift.tt/3gJ7ALD

Polarity, Resonance, and Electron Pushing: Crash Course Organic Chemistry #10:

We’ve all heard the phrase “opposites attract.” It may or may not be true for people, but it’s definitely true in organic chemistry. In this episode of Crash Course Organic Chemistry, we’re learning about electronegativity, polarity, resonance structures, and resonance hybrids. We’ll practice a very important skill for this course that will help us avoid a lot of memorization in the future: electron pushing. It’ll be a lot of trial and error at first, but we all start somewhere!

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