General Chemistry

What you will learn in this part...

  • Discover the atomic world
  • Explore a smorgasbord of elements
  • The relationship between electrons and bonding
  • The key chemical reactions you will face during the PCAT
  • The Rules of Thermodynamics

All the medications ever made, start from a rudimentary chemical process. General chemistry is the study of their base components, known as elements. Chemistry and organic chemistry are essential sciences in your journey towards becoming a pharmacist. Organic chemistry is a subset of general chemistry and focuses on molecules that are made up of carbon, whereas general chemistry is pretty much everything else. Human beings are carbon based. So too is the food we eat, the clothes we wear and the book you are reading. When carbon is mentioned in this context, this is not to say the food you eat or this book for that matter is a lump of coal, but comprise of molecules whose primary constituent is carbon.

The science of chemistry is mainly concerned with the study of the properties matter, these properties can either be qualitative (such as how they react, or smell) or quantitative(such as things you can objectively measure such as temperature or state). These can be further subdivided into two main categories, physical properties and chemical properties. A physical property is a characteristic of a substance, which does not change when you measure it. For instance, a physical property of water is whether it is a solid, liquid or gas, or what temperature it transitions between these three states, or density (the concentration of solid matter in a solid substance) which can be defined as follows:

How to calculate density

A chemical property is less personal and describes how a substance interacts with another and the changes that result. For instance, hydrogen burns in oxygen to produce water.

To better understand general chemistry and the way that base elements work with or against each other is much easier with a basic understanding of how simple atoms interact to become bigger collections of atoms bonded together called molecules.

Atomic Theory

Atomic theory describes the tiny individual atoms that make everything into something, known as matter. Atoms typically have three main constituent particles, neutrons, electrons and protons, in various quantities. It is the quantity of each of these three and the way they do or don't combine with other elements that makes each form of matter unique. In fact the word "atom" actually derives from the ancient Greek adjective "atomos” which means indivisible (suggesting there is nothing smaller), however, this is not strictly true, as advanced as they were the ancient Greeks did not invent an atom smasher. Each proton and neutron comprises of three quarks, two up quarks and one down quark. A strong nuclear force sticks the quarks together. Most of the mass of a proton and neutrons comes from this strong nuclear force, rather than from the quarks.

Each atom of matter, will have at least one part that has a positive electric charge, this is called the proton. The negative part is called the electron and the neutral part is called, funnily enough the neutron. If you add how many protons and neutrons you have together you get the atomic number (Z), which is used in the classification of the element.  

Z = neutrons + protons

The structure of an atom can be described using the nuclear model, which describes an atom's nucleus, which is where, the nucleons: neutrons and protons live; surrounded by a cloud of electrons hovering above (see Figure 11-1). The one exception to this is hydrogen, which somehow manages just fine, without any neutrons. The electrons stay close to the nucleus because of electromagnetic force.

Atomic structure.

Figure 11-1: Atomic structure.

Atoms can be attached to each other via chemical bonds; these are formed using electrons to make up a molecule. When the number of neutrons in the nucleus is increased or decreased, something called an isotope is formed. Although there can be lots of different isotopes of an element, its atomic number won't change because the number of protons isn't changing, however the mass numberwill change. The mass number is another useful categorization tool that chemists use and describes how many neutrons are contained within the atoms nucleus. So to find out how many protons in the nucleus you can use this equation:

Number protons = Atomic number - Mass number


All protons, everywhere in the universe, like all other atomic particles are exactly the same, and pretty much all of them are inside atoms. Different atoms have different numbers of protons; what makes an atom be a nitrogen atom, or a silver atom. Protons make the nucleus, or center, of an atom. The simplest atoms - hydrogen atoms - have a nucleus made of just one proton. But most atoms have more than one proton, and at least one neutron to go with each proton.


Electrons, have no parts and pieces (they are tiny, only 1/2,000th the size of a proton) and carry a negative charge. If you want electricity or a working magnet, you'll need electrons to make it happen. Although tiny, they are not insignificant as the electrons, in an individual atom will determine its chemical properties and will also affect its magnetic properties. The advanced science known as quantum physics is focused on the study of atom properties. In a stable element, the amount of electrons is always the same as the amount of protons, if this differs the atom is called an ion. Electrons, not only provide charge but a means by which multiple atoms can bind together, when this occurs the substance is called a compound, which is an electrically neutral (protons=neutrons) substance. When they contain carbon they are deemed organicwhen they do not contain carbon they are called inorganic.


Neutrons are the mediators in an atom, and are pretty much identical to protons (they have the same weight) except, that they carry no charge. A protons positive charge balances an electrons negative charge and the neutrons are a bit boring as they have no charge.

Quick Question

If an atom, is described as an isotope, which of the following options is the best description?

A. The ratio between electrons and protons is not 1:1

B. The atom has more or less neutrons than its natural state

C. The ratio of protons to neutrons is 2:1

D. The atomic number and the mass number is the same.


If the ration of protons to electrons differs this would mean the atom is deemed an ion, which would have an overall charge, therefore this rules out options (A) and (C). For option (D) where the atomic number and mass number is the same this scenario is near impossible as the atomic number is how many protons plus how many neutron and the mass number is how many neutron, this would only be applicable if there were no protons, which is quite rare apart from in some Hydrogen atom, so this answer is possible but maybe not the best definition. (B) is the best answer here as an isotope is an atom which has differing amount of neutrons in its nucleus.


















The Periodic Table - Key Classifications

The ratio of the different atomic particles within an atom i.e. the ratio between protons electrons and neutrons gives the atom certain characteristics like, how reactive it is. Reactive, is a measurement of how well an atom interacts with another atom. When the atoms are stable and they don't break down in to their constituent atomic parts, the atom is called an element. Elements are catergorised into a table called the periodic table, which is seen by many scientists as a useful, well-designed grouping of all of the elements that have been encountered throughout the history of modern chemistry.

Periodic Table

Figure 11-2: The master of categorization, the periodic table.

The table lists elements, next to other similar elements and organizes them using their atomic number.

The periodic table is occasionally updated, when science discovers or creates new elements. Yes, elements can now be artificially created! Scientists can use a machine that combines protons and neutrons to make novel unnatural elements (although these are often unstable and break down almost immediately and have pretty much no practical use). The 100+ natural elements, leave room on the table for a couple dozen more artificially created ones, but the table will need to be redesigned after that, so expect changes.

How to turn lead into gold - the modern version of alchemy

Alchemy, is a ancient science (derived from Arabic - Al - the and -chemy meaning science) where "scientist, magicians, alchemists or lunatics” searched for how to create ever lasting life, via the Philosophers Stone or gold, to make a bit of money on the side. Although they did not have much success, the myth has become a reality as modern chemists have discovered how to make gold from pretty much anything.

Scientists can create or alter any element by either removing or adding electrons or nucleons to the element's composition, causing its chemical properties to change. In fission reactions, which are those that take place in atomic bombs and nuclear power plants, large atoms can be split into smaller atoms. When this happens they release a huge amount of energy. To create atoms, the scientist needs to do the opposite i.e. apply a huge amount of energy to combine particles to make an atom. All you need to build an new atom is to add protons or neutrons to the nucleus of any element you choose. If you can put two smaller elements together, you can fuse them into a larger element such as gold. The only down side is that the energy required to make an atom of gold outweighs the commercial value of the gold atom that is made. Hopefully, one day, when energy is cheap enough the benefits will outweigh the costs and we will have cheap gold so rappers wont have to pay so much to get bling grills.

The periodic table is arranged by order of increasing atomic number in such a way that the periodic properties (chemical periodicity) of the elements are made clear. The standard form of the table, includes periods which are the horizontal rows in the periodic table and groups which are the vertical columns. Elements in groups usually have similar properties to each other. There is no single or best structure for the periodic table and they sometime differ but by whatever consensus there is, but the classical periodic table is seen as a useful way to visualize the smorgasbord or elements available to a chemist.

The main elemental groups

Strictly speaking the main groups comprise of the taller columns of the periodic table i.e. Groups 1-2 and 13-18, see figure 11-3 below, however we grouped the Transition metals and Group 12 for ease of use in this section.

PCAT periodic groups

Figure 11-3: The main functional groups.

Elements that have similar characteristics are kept together in these main groups, the layout of the periodic table is such that similar molecular properties line up nicely into vertical columns due to similarities in their electron structure. Some of the groups have eight members and others have more or less. A simplified way to look at the elements is to classify them as metal, metalloids and nonmetals (as seen in figure 11-3):

  • Metals - are shiny, conduct electricity and are bendable.
  • Metalloids - sit in between the two, have some metallic properties but have chemical properties similar to nonmetals.
  • Nonmetals - do not conduct electricity and are brittle.

This is a bit of an over simplification and for the PCAT you will need to know some of the key groups in a little more detail. The official main groups, you will need to know before attempting the PCAT are:

  • Nitrogen Family - the key players in this include nitrogen, phosphorus, arsenic, antimony and bismuth.
  • Halogens - elements included are fluorine (F), chlorine (Cl), bromine (Br), iodine (I), and astatine (At). Often live as diatomic molecules, meaning they naturally live in bonded pairs like Cl2
  • Nobel gas family - a lot of these you will know like neon in luminescent lights and helium in balloons. Others include krypton (yes like Superman!), radon and xenon.

The Nitrogen family and the Oxygen family

Group 15 of the periodic table, known as the nitrogen family. As it is a distinct element group elements here have different proton and electron configurations giving them different properties. Nitrogen is all around us, odorless, colorless and non-flammable. Nitrogen occurs in nature through amino acids and macromolecular proteins in humans, plants and animals and in remains of very old plant life that has fossilized.

Phosphorus, like nitrogen, is nonmetallic and is just outside the ten most commonly found elements on earth. Pure phosphorus is not found anywhere in the natural world, but rather is a component in the form or ores. These ores are most commonly used as an ingredient in fertilizer because they provide significant nutrients to growing plants. Phosphorus is commonly seen in its white toxic and red nontoxic forms. Both are flammable as you can see when you strike the average matchtip. When mixed with other chemicals and compounds, phosphorus is used in plastics, nylon, motor oil, soap and detergents. It is also mixed and used in cheese, soft drinks, instant oatmeal and baking powder.

Arsenic is a metalloid in that it is not quite a metal and not quite a nonmetal. Arsenic is very poisonous. and so is often used to kill weeds and bugs in low concentrations. Arsenic is usually found in sulfides that contain it, although not all sulfides will have arsenic in them.

Antimony shares the metalloid trait with arsenic and is often joined with lead to create batteries. Antimony and arsenic also share another trait. In their oxide form, where oxygen is included in the compound, antimony and arsenic are neither an acid or a base, having a neutral PH value. We'll speak more about PH further on in this book, but most elements, in their oxide form will either be an acid or a base.

Finally, there is bismuth. This element is the one metallic element of the nitrogen family. You might not have heard much about bismuth, but it is a frequent ingredient in medications and cosmetics. In make-up, bismuth is important because it has a shine and it connects well with the human skin. Bismuth is used in medications that treat digestive discomfort, like Pepto-Bismol (now you know where that funny name comes from). It's interesting to note that science doesn't really know for certain why bismuth can calm an upset stomach or reduce diarrhea, but it definitely works.

The Halogens

Fluorine, chlorine, bromine, iodine and astatine make up the halogen family of the periodic table. One unique feature of this group is that the elements represented, unlike all other groups of the table, are all demonstrated in three of the four states of matter, those being gas, liquid and solid at standard amounts of pressure and temperature. Fluorine and chlorine are a gas, while bromine is a liquid. The others are all solids. If you want to make an acid, you just add a halogen family member to hydrogen. This family is produced from minerals. All halogens are toxic and nasty.

Fluorine has an atomic number 9, which makes it the lightest member of the halogen family. Fluorine is used as a refrigerant (freon is what makes air conditioning so cold) and also in the processes for making steel and aluminum.

Additionally, fluorine is used to enrich uranium if someone wants to build an atomic bomb. Pharmacists come across fluorine everyday in their professional lives as it is present in drugs including Fluoxetine (Prozac(c)) and Atorvastatin (Lipitor(c)). Fluorine is also abundant in local water you local water supply and your tooth paste as it can help strengthen teeth.

Chlorine is used for many things beyond swimming pools, including laundry bleach, plastics, disinfectants and a lot of other consumer products. The salt you eat or use to melt snow has chlorine in it. Unfortunately, chlorine has also been used as a weapon by humans in the form of chlorine gas.

The next member of this family is bromine. Bromine is the liquid of the family and it also smells pretty bad (Greek- bromos- stench). It will also give you a very nasty burn if it finds your skin. Bromine can be found in brine, or salt water pools. These pools are often created to preserve food, age cheese or create that "pickled” flavor.

Bromine was commonly used in fertilizer until it was discovered that its gas depleted the Earth's ozone layer. Bromine is used in the manufacture of gasoline as it reduces the "knocking” in vehicle engines. Some oil and natural gas drilling solutions use brine and therefore bromine. If you have a fondness for Mountain Dew, you are enjoying its citrus taste thanks to brominated vegetable oil.

Another solid member of the group is iodine. Iodine gets its name because of the purple color of its vapor when heated. Iodine, like bromine, is found in brine pools and is commonly used as a contrast material for x-ray and other medical imaging.

Unlike most of the other group members, iodine does play a role in human biology. Thyroid hormones use iodine to synthesize, so iodine is most commonly found near the thyroid gland in the human body.

Iodine is used as an important nutrient in livestock feed and as a disinfectant for water treatment. Silver iodide is used to seed clouds, encouraging them to product rain. Unfortunately, iodine is also used to manufacture methamphetamine.

Astatine is the final halogen family member. It is very radioactive. In fact, no one has ever seen astatine because any attempt to make it visible would be consumed by its own radioactivity. The youngster of the family, astatine was discovered in 1940. Scientists always knew it was probably there and the space reserved next to iodine for it was known as "eka-iodone”, or one step below iodine.

It doesn't last very long, but astatine is very important to modern medicine as it is used for highly targeted radiation therapy, particularly for treatments of the thyroid.

The Nobles

The noble family of elements is all gases and is made up of radon, xenon, krypton, argon, helium and neon. They don't have any color or smell, but they affect us in many ways.

Radon is a gas that is produced as radioactive materials decay. As such, inhaling too much radon will almost guarantee cancer somewhere in the respiratory system and only smoking causes more lung cancer.

Radon is sometimes found leaching through basements in homes and other structures as it leaches through cracks in flooring and travels in the water stream, but this is most common in Iowa and Pennsylvania and there are testing products available at hardware stores and big box home improvement stores.

Radon is produced as a product for use in radiation therapy, primarily in cancer-fighting "seeds” that are implanted near the cancerous growth.

Xenon is used to make the bulbs that your neighborhood movie theater probably uses. So-called "xenon” headlights are also a newly popular auto and truck product. If on the other hand, you're really just looking to add some serious horsepower to your next spacecraft, xenon has been proven to be your best propellant.

Xenon is easy to make if you take air and separate it into oxygen and nitrogen because the liquefied oxygen will also have xenon and a bit of krypton. Xenon is also present in some lasers use to treat skin problems. But, in medicine, xenon is primarily now being used as anesthesia, particularly in Europe. It is also used for medical imaging.

Krypton, like most of the noble family members, is well-suited for lighting. We're not really sure why it would hurt Superman, but apparently it does. It makes a great photographic flash, especially when a high-speed camera is being used. Despite a name that might suggest otherwise, krypton alone is often the gas that lights up in "neon” lights and it's also found in certain lasers that require a red light.

Argon gas is very common in the Earth's atmosphere. You may have heard of argon welding equipment and argon produces a bluish green color when it's highly heated. Argon is used as a fire suppressing gas for server rooms because it can suffocate a fire without any damage to the equipment.

Argon is used by the food industry to displace oxygen, thus helping food to last longer in its packaging and helps paint to last longer after you open the can.

To Americans, argon has a special place because it is used in special containers to preserve and protect some of our most important historic documents, including the original Constitution and Declaration of Independence.

Lasers with that bluish green color are used to zap small tumors and for various eye surgeries as well as for "welding” arteries. Argon fills incandescent light bulbs and fills the space between glass panes in highly energy efficient windows.

Helium is fun at parties, but has many other practical applications as well. Helium is found throughout nature, but especially near natural gas pockets. Helium is used for welding, known as "arc” welding. It is also used by the semiconductor and silicon wafer manufacturers.

In medicine, helium is usually used to cool the magnets in magnetic resonance imaging (MRI) scanners. It is also used in cryogenic applications, including leak detection and may also be used to help deep diving scuba divers breathe easier or to help them move nitrogen out of their bloodstream if they get a case of the "bends.”

The final noble family member is neon. As we wrote earlier, most "neon” signs have other noble family members included, because neon by itself can only be red, orange or red-orange when left alone in a neon tube. Neon is also used in some laser applications, vacuum and television tubes.

Transition Metals

The 38 transition metals of the periodic table get their name because they can have several states. This is due to an incomplete shell and changes in the electrons they use when they are combined with other elements. Several of the transition metals are names you have probably heard of, such as titanium, iron, nickel, copper, zinc, silver and gold. But, when was the last time you heard anything about rutherfordium? Let's take a look at this family in detail.

Unubrium is a very new element, only discovered in 1996. Like some of the other transition metals, unubrium does not occur naturally, but rather is synthesized by scientists. These man-made elements include unununium, ununnilium, meitnerium, hassium, bohrium, seaborgium, dubnium and rutherfordium,

Mercury has also been known as quicksilver. Mercury shares a distinction with bromine, in that it is a metal, but lives as a liquid at normal pressure and temperature conditions.

Mercury is used in many medical devices (remember the syphgmomanometer?) including thermometers, float valves and manomaters, although much about these instruments has been replaced with digital technology and the continued sale of medical or other devices containing mercury has been banned.

Mercury had a higher use in medicine until its toxic effects were uncovered. There are still places around the world that use a skin wound treatment that includes trace amounts of mercury.

Fluorescent lamps contain mercury and they light when the mercury vapor gets excited by electricity. Many "neon” signs include mercury for specific colors. Mercury is also used in mascara, but its use here is also on the decline.

We'll skip over the value or mining of gold, but it has many applications in our world beyond currency and jewelry. Gold is frequently used by dentists to make teeth and crowns. Gold is also added to some biologic specimens to aid in viewing by a microscope.

Gold flake is added to foods, so you can drink gold if you don't mind paying a small fortune for a cocktail. It won't be absorbed and it will leave your body exactly as it came in, which might make for some interesting bathroom conversations. Gold is also used to connect metal objects as a solder and sometimes made into a thread. You'll also probably find gold in some of your video and audio cables because it doesn't corrode and it conducts electricity very well.

Platinum is actually more rare than gold, but its uses are more modern and it doesn't have the perceived value of gold. Beyond jewelry, platinum is most often used in the catalytic converters of vehicles because it further reduces vehicle emissions. You'll find platinum in many medical instruments and laboratory containers.

When you need a tough metal, osmium may fit the bill. Osmium is used the tips of pens and it used to be used for the "needle” on record players, but it doesn't have many notable medical uses.

Tungsten is another "tough” metal, often used for industrial knives, drill bits and cutters for tough industries like petroleum and mining. Tungsten is also the transition metal of choice when a casing is needed around very high heat, such as for the exhaust of a rocket ship.

Tantulum is probably inside your cell phone, laptop and car stereo as it often used as a protector for electrical components that are very small, but it has been used for coating human body implants.

You're probably most likely to know cadmium for its role in rechargeable batteries, but it also has uses including fluorescent microscopes.

There are a few medical uses for sliver. You will find it used in endotracheal breathing and urinary catheter tubes as it is thought to reduce infections related to the devices themselves. It is also commonly used as a coating on other medical devices and for wound dressings. A sister of silver known as colloidal silver is heavily marketed to cure just about anything, but modern science doesn't put any credence to these claims and there can be some bad allergic reactions when colloidal silver is taken with certain prescription medications.

Palladium is commonly used in the blood test strips needed by diabetics, as well as being used to manufacture instruments used by surgeons. It is also used by dentists for implants.

Rhodium is used in the manufacture of the crucibles you might encounter working in a laboratory, but it's more commonly found being applied as a filter for mammography equipment.

Technetium is an important transition metal for medical testing. It is often used in "tracers” that are introduced into the human body, clearly identifying a tissue or organ for medical equipment. In this role, and as a possible pharmaceutical specialty for you, it is known in a group named radiopharmaceuticals.

Molybdenum is a key ingredient in human teeth, as it helps to prevent tooth decay in the enamel. We eat this transition metal when we consume eggs, pork, lamb, sunflower seeds, cucumbers, lentils and other grains. Diseases that cause low molybdenum levels will affect certain enzymes that help the body work with nitrogen.

Many medical devices that will be spending a long time in the human body, including pacemakers, will include nobium. This transition metal isn't typically affected by biologic processes, maintaining an inert state, so it doesn't create any reactions when introduced into the human body. Known to be hypoallergenic, niobium is also found in jewelry.

We don't recommend you buy an engagement ring made with zirconium, but you will encounter its use in medicine. Nuclear medical imaging gives doctors the ability to see body processes as they function and in 3 dimensions. This testing is now commonly known as PET scanning and zirconium makes it possible.

Yttrium has some specialized medical uses. When used as an isotope version of itself, yttrium creates needles able to cut extremely precisely, such as when a surgeon needs to cut spinal cord nerves. Yttrium is also often used to attack cancer cells with highly localized internal radiation.

Simply put, we need zinc. Zinc has several jobs, including helping individual cells know when it is time to die. Zinc is also associated with many of the proteins in our body and helps us learn. We can eat foods to maintain zinc levels, including red meat, lobster, nuts, seeds, celery and foods fortified with zinc or multi-vitamins with added zinc.

Low zinc levels are frequently found in humans suffering from sickle cell disease, chronic liver disease and diabetes, many of whom exhibit symptoms such as low appetite, impotence, diarrhea and altered mental functions as well as impaired ability to fight infection and disease.

The human body uses copper to transport and process oxygen and to help the body use iron. You'll also find copper in construction materials where germ control is important, such as railings, faucets, door knobs, computer keyboards, and the handles on shopping carts and toilets.

Without iron, human beings would be doomed. Iron helps the human body make red blood cells and blood cells carry oxygen throughout the body. Enough said? The problem with iron is that the human body only receives iron if we eat foods that contain it. Iron deficiency is a common problem that will cause sluggishness, dizziness and problems with attention to detail. Women are particularly prone to iron deficiency, often because of menstruation. Iron is found in many foods, including red meat, fish, poultry, lentils, many vegetables and tofu. Humans who have chronic problems with low iron will usually resolve symptoms with a supplement or iron-fortified multi-vitamin.

The human body seems to tolerate titanium very well, so it is used to manufacture replacement joints and other medical implants. Titanium is also used for many of the tools that surgeons and doctors use because it is light, easy to sterilize and has long lasting strength.

How do we know an electron rotates?

Electrons are always on the move. Often called electron "spin,” this movement is actually a very tight loop. If electrons didn't move, they wouldn't have a negative charge or produce a magnetic field. We could digress here into a long paragraph about electron movement or anti-movement, but let's stop with making sure you understand that electrons move and add that the pattern of this movement is a mathematical function known as the atomic orbital.

Using atomic orbital math, you can calculate, with certainty, where in a atom's nucleus an electron might be. Now, you need to meet the photon. If you're a Star Trek fan, you'll remember Captain Kirk calling for the photon torpedoes to be fired at Klingon spacecraft. This isn't a bad example because a photon is the carrier for force, including electromagnetic force, radiation and light. Photons are found in classes related to their mass, spin (like the electron kind) and electric charge. Albert Einstein was the early creator of the photon concept, but we are still discovering the math that explains science we don't yet understand.

Photons can't sit still and they have no mass. I photon can be given, as is the base with gamma rays or it can be taken away during an atom's temperature change. In a perfect world, photons would move at the speed of light. Current science believes that they always do and that any "slowing” we might note is actually changes to the photon's momentum and wavelength, also known as a phase shift.

Orbital energies

In atomic physics and quantum chemistry, the electron configuration is the distribution of electrons of an atom or molecule (or other physical structure) in atomic or molecular orbitals.

Electron affinity

Electron affinity is the amount of energy that is released with an electron is attracted to an atom. Some atoms really want to grab electrons as they travel by, like a frog's tongue to passing insects. Fluorine is an example of an element whose atoms love to grab electrons from nearby sources.

Lightning is an event where electron affinity is easy to visualize. The bright flash we see is electricity being discharged. The ground, or in some cases a tree or other matter, is willing and wanting the electrons that are traveling within the lightning.


Electronegativity is the exact opposite of electron affinity. Atoms that display electronegativity will give electrons away. Francium will easily give away electrons. In our lightning example, the clouds and atmosphere want to give away electrons and the lightning is a search for a willing recipient.

The Building-up Principle

When science wants to find an atom, molecule or ion's electron configuration, they turn to the building up principle, also known as the Aufbau principle. According to this principle, electrons will not fill orbitals with high energy levels until the lower energy levels are filled.

Before moving on, we need to introduce the Pauli exclusion principle. Under this quantum mechanical principle, you will never find two identical particles sharing the same space in the same state, or quantum state.

So, since electrons can't share the lower energy space, they will move to the next highest energy and receptive atom and join there. This model can also be used to guess what the proton and neutron configuration of an atom's nucleus will be.

Finally, when atoms that have formed molecules decide to attach to a molecule with different atoms, we know this as a compound.

Bonding for Better or for Worse

When atoms, molecules and compounds want to stick together, they need some help in the form of bonds. Bonding is affected by the electrons being taken and given away. All elemental atoms, except the nobles, want to have a perfect outer shell. The nobles are excluded because they already have this perfect shell. Most of the rest of the elements follow the octet rule that states that they can't be perfect until they have eight electrons in their shell.

A few elements, including hydrogen, lithium, boron and a couple others find perfection with only two electrons, following the duet rule. Whether following the octet or duet rule, elements are actively searching to perfect their outer shell and there are several bonding types they use.

Chemical bonding

When atoms attract different atoms to form a chemical substance with two differing atoms, this is known as chemical bonding. There are a couple different types of chemical bonds.

Covalent bonding

Covalent bonding is known to be the simplest chemical bonds. In a covalent bond, an electron or two are attracted into a space between the nuclei of two nearby atoms. These electrons really want to join both nuclei instead of just jumping towards one or the other, so the nuclei, and therefore the atoms are held in place. Although this can happen in other bonding types, the key is that the sharing of the electrons is equal, or balanced in both nuclei.

If the electrons are not equally shared between the nuclei, the attraction is known as a polar covalent bond.

Ionic bonding

Ionic bonding is a different form of bonding that is not chemically driven, but rather occurs because of a difference in the ability of two atoms to attract an electron. These bonds are pretty tenuous and are easily broken with the addition of water.

The other type of bond is the hydrogen bond. Only oxygen, fluorine and hydrogen can use the hydrogen bond. Water is an example of a hydrogen bond. Because of the hydrogen bond, hydrogen and oxygen move slightly from their positive or negative polarity so they begin to repel other hydrogen or oxygen atoms and join to each other.

Knowing the Appropriate Reactions

With elemental atoms trading electrons and bonding, science strives to understand what the reactions of the atoms will be. Let's look at each of these reactions.


Synthesis is a reaction in which two or more compounds come together and form a new and more complex compound. A simple example would be a peanut butter and jelly sandwich. When bread, peanut butter and jelly are combined, a new item, called a peanut butter and jelly sandwich is formed. None of the ingredients have changed or merged with each other, but they join together to form something else. This is synthesis.


Decomposition is the opposite of synthesis. If you love Oreo cookies, but you don't love the crème in the middle, you might scrape the crème out and enjoy the cookies. You have decomposed the cookie.

Single Displacement

In single displacement, elements from two or more compounds trade places with each other. If the jelly jumped off the peanut butter sandwich and onto the oreo and the cookie crème jumped onto the sandwich, this would be a simple example of a single displacement.

Double Displacement

Like its name, double displacement shows portions of different compound molecules switching places to form new and completely different compounds.

Acid-Base Reaction

Sometimes, a compound that is acidic and one that is non-acidic, or base, will react with each other. This type of reaction will most likely produce some salt and water as the positive and negative ions react.


The final reaction is combustion. When heat is created by the reaction, this is a combustion reaction.


We mentioned ions earlier, but we need to go one layer deeper to understand the replacement reaction. Ions, as you'll remember, are atoms or molecules where the electron numbers are higher or lower than the proton numbers.

An anion is an ion with a negative charge. It has fewer protons than electrons. A cation is just the opposite and carries a positive charge. Anions tend to end their names in -ide, such as sulfike, nitride or fluoride. Cations don't have a typical naming convention, but lead and iron are both cations.

In the case of a replacement reaction, two cations combine with a single anion after trading places. One of the cations will create a compound and the other will be ejected from the compound. There are single replacement reactions and double replacement reactions.

pHooling around with Acids and Bases

All substances are either an acid or a base. Acid substances are identified using three definitions. The Arrhenius definition says that a substance that will increase the hydronium ions if mixed with water. The Bronsted-Lowry definition says that acids are those that like to give away their protons. Finally, the Lewis definition says that a substance that wants and likes to accept electron pairs is an acid.

Touching base

Bases, on the other hand, are the exact opposite to acids. They use the same three definitions, but in reverse. So, as an example, a base as defined as a Bronsted-Lowry defined solution would be one that attracts photons versus giving them away.

Try not to touch acids

Bases, unlike acids, can be handled with your bare hand and will tend to feel squishy or slimy. Because acids are caustic, you don't want to handle them without protective equipment. Acids will react to bases and also with metals. Acids will also tend to taste sour.

The pH Scale

All of these solutions need a uniform measuring system and that system is pH. The pH system is a scale with highly acidic and highly base solutions at opposite outside ends of the scale. Some say that pH stands for the "power of hydrogen,” but there's no factual evidence to support this. All branches of science have agreed on a standard measuring system internationally. There are many devices available to test the pH value of a substance from simple dip strips to extensive digital sensors.

Acids and base compounds are measured based on the number of hydrogen ions (positively charged) or the number of hydroxide ions (negatively charged).

Water, and specifically pure water, has a pH of 7. Any solution with a pH less than pure water is an acid and any with a higher pH is a base, also known as an alkaline.

Chemical Equations

Chemical equations are a way to represent what science is seeing in various reactions. On the right side of a chemical equation is the output, or the formed substances and the originating substances on the left side separated by a right arrow that is known as yields. You might also see other symbols, such as two parallel horizontal lines for stoichiometric reactions, opposing horizontal arrows if there are bilateral reactions or others.

The original and reacted states of substances will often be shown in their physical state, be it aqueous, gas, liquid or solid and parenthesis or brackets. The Greek capital letter delta will be added if the reaction needs energy.

Equilibrium and reversibility

Sometimes, the reaction will also have an opposite "un reaction” and this is called equilibrium. The reaction is both directions will take approximately the same amount of time. Ultimately, there is no net change during or after the reaction because whatever was done was also undone.

Conventions and golden rules of chemical equations

When you are writing an equation, remember these golden rules:

  • The chemical reaction arrow, → , indicates "yields" and shows the course of the chemical activity.
  • A delta symbol, (D), above the arrow sign that heat has been introduced into the reaction.
  • A twofold arrow, ↔ , indicates that the response is reversible and can go in both headings.
  • The diatomic components when they stand molecularily distinct from other molecules else are dependably composed as follows: H2, N2, O2, F2, Cl2, Br2, I2
  • Adjusting an equation so that it is balanced, should be finished by setting coefficients before the equations to guarantee the same number of particles of every component on both sides of the arrows.
  • When starting to equalize an equation, check every formula to see that it is right. Never show signs of change an equation when adjusting of it for accuracy.
  • Assuming that a reactant or item is solid an (s) is put after the distinct chemical.
  • Assuming that a reactant or item is a gas, a (g) should be put after it.
  • Assuming that a reactant or item is in an aqueous phase the symbol (aq) should be put after it.
  • Balancing chemical equations

When constructed a chemical equation, it's important to ensure that the equation is balanced. A balanced equation is one where the same number of each atom type appears on each side of the equation. This is done because modern science believes that atoms are not changed, added or lost in a chemical reaction, but rather just shifted.

Mass - Feeling the Weight of the World

There are several definitions for mass. If you want to know how much energy it takes to move an object, you would calculate its inertial mass. If, however, you were interested in how an object reacted to gravity, you would study its gravitational mass.

Molecular mass

Another measure of mass is molecular or molar mass. Although there are a few flavors of this as well, we'll use the term generically. As we have discussed, chemical reactions create molecules. We also know that the periodic table shows the atomic weights of the elements. So, we can work with either the average molecular mass using the periodic table or calculate molecular mass by adding the individual masses for the isotopes for a particular atom.

You can also calculate molecular mass using mass spectrometry. This test will use the most common isotope in determining the molecular mass. The good news for you as a student and as a practitioner is that there are excellent manufacturers of instruments that will provide you with a molecular mass whenever you need one.

Moles and how to move between mass units

The metric system is the common standardized measuring unit used by all the sciences worldwide. You may want to think in pounds but for comparability and reference only the metric should be used. One such unit that is used in mass calculations is the mole. A mole should be seen as any other measurement, for example, a centimeter represents a set distance, a kilogram represents a set weight and a mole represents a set amount of atoms, which is 2.0 x 1025, called Avogardos constant. If you were to calculate the exact number of atoms in say 12 grams of Carbon-12, you would be hard pressed if you didn't have a scientific calculator. So moles are a handy way so you do not need to handle a number the length of a toilet roll. Sometimes, this is hard to grasp, but just imagine a mole as a standardized cup of measurement, holding a set amount of atoms like marbles. The larger the marbles in the cup, would mean the less of them that can fit, conversely the smaller the atoms the more that can fit. This is exactly the same for atoms, atoms of different elements will take up a different space within the mole and therefore there will be more or less of them accordingly.

If you learn anything about moles, learn this equation:

Holy Moley

The number of Moles in a sample is equal to the sample mass (in grams) divided by its molecular weight.


How many moles in 2 grams of Sodium Chloride (Na=23, Cl=35.5)?

A. 0.3 moles

B. 0.34 millimoles

C. 3.42 millimoles

D. 34.2 millimoles


Firstly, the examiner is assuming you know the chemical equation for common table salt, you should, its NaCl. Once you know this you know you can get the molecular weight by adding Na+Cl. Then you need to plug these figures into the Mole equation:


So the answer is option (D). The units can be a little confusing, but all you have to do is multiply the answer by 1,000


Thermodynamic scientists spend their time studying heat, work and energy. They look at items such as pressure, internal energy creation, temperature and entropy, or the flow of energy through a process.

There are four laws that are applied in thermodynamic study. The first law establishes that a system has an internal energy that is distinct from heat or work and that energy in the universe always exists, so it can neither be destroyed, nor created, but only transferred.

The second thermodynamic law states that whenever there is a transfer or energy, some or all of the energy becomes a bit less useful. As an example, think of what happens in an explosion. The energy closest to the blast site sees tremendous energy, but the further you are from the blast site, the less energy you experience because it is expanding outwards. The second law says that energy always wants to expand, thus diminishing its power, even though it is not lost. Put a pot of tea on the stove for a second example. After the teapot has boiled and you turn off the heat, what happens to the temperature of the boiling water? The heat energy wants to expand into the surrounding space and you can feel this in the steam rising from the teapot as it cools.

Chaos is the rule for the third law of thermodynamics. Based on entropy, or the acceptance that energy prefers chaos over order, the third law states you will never get the entropy, thus the energy, of anything to a state of complete stop with a finite number of operations. Or, the entropy of a system will never quite reach zero unless it is taken to absolute zero.

Law of thermodynamics number four is, in our opinion, still being developed, but it focuses on outer space and dark energy and its seeming effect on the expansion of the universe.

What is energy?

Energy seems easier to "understand” than it is to define and it is often spoken of in its delivered form, such as radiant energy, kinetic energy, chemical energy, electric energy, magnetic energy or potential energy. We know that work, in the science world and our everyday lives, requires energy, so we know it's there to be used or stored for future use.

Radiant energy is the energy used (we're trying to stay away from "created”) by electromagnetic waves and its measured in joules. You'll find radiant energy mentioned in discussions about lighting, solar and other heating and telecommunications.

Kinetic energy is the measure of motion-produced energy. So, if the car you're riding in suddenly stops, you'll probably feel yourself pressed against the seat belt because you and the car have different kinetic energy. It is also measured in joules.

When a single or set of chemical changes causes a substance to change, it is the result of chemical energy. When you pull the chain on a lamp, the light bulb will emit light as the result of chemical energy.

Electric energy and magnetic energy are closely aligned. Take the doorbell as an example. When the doorbell is pressed, it creates contact for an electromagnet with a metal bar and the bar swings to ring bell. In this example, the electric energy in the doorbell button triggers the magnetic energy in the bell mechanisms.

Potential energy is a bit different, because it measures the energy that an object might have only because of where it is. If a force, or set of forces (let's call it a force field) acts on the object and the object moves to a new position, the measure of the distance travelled will become known as the potential energy.

States, systems, and energy

When dealing with matter, there are four states, including solid, gas, plasma and liquid that are easy to observe and a couple you would only find in very, very cold or very, very dense matter.

When an object is solid, obviously, its particles are tightly packed. Although the particles can still vibrate, they can't move around like they might want to. The simple way to change the state of a solid is to heat it up to a liquid or freeze a liquid back down to a solid.

 You might be able to contain a liquid, but you'll never get it to cooperate like a solid will. But, liquid has a unique property that the other 3 states don't share. The surface of a liquid can resist an external pressure.

This would explain why a giant cargo ship full of shipping containers that is clearly much heavier and much denser than the surrounding water can easily float across the water's surface. If you've ever seen a video of a reptile or insect "running” across the water, this same principle is at work.

In a liquid, the molecules are being tugged in every possible direction, except on the surface. As the molecules are tugged into the water's body, surface tension is produced.

From a liquid, additional heat energy will produce a gas. Gases can pure, like one of the nobles, or can be a mix of several different elements like the oxygen we breathe. Gas particles have lots of elbow room, so their bonds are much more tenuous than a liquid or solid, allowing free range of motion unless captured in a vessel. Gases are frequently described by the properties they exhibit, including temperature, pressure, number of particles or volume. In the temperature description, gas is described related to how it expands or contracts when heat or cold is aimed at the gas. When you see a helium balloon that is shriveled and appears to be losing its gas, what you are experiencing may also be attributed to the helium becoming denser in a lower temperature.

Finally, when a gas contains particles that are carrying a positive or negative charge, it becomes a plasma. This specialized gas will have a strong reaction to a magnetic field, unlike other gases. Plasma is what is actually happening in a lightning bolt and also in most "neon” lights. Plasma cutting has become a popular choice because it gives the user precise control over the shapes being cut from metals and plasma televisions use the magnetic reaction of plasma gases to display a very sharp picture.

Enthalpy and entropy

At a constant pressure, there will be a difference in the energy that is used to disconnect chemical bonds and the energy that is collected in the newly formed bonds that are created by a reacton. This is called an enthalpy change.

If you remember our conversation about the second law of thermodynamics, you'll remember that we mentioned entropy as the desire of energy to move away from order and into chaos. This is often called dispersion. Entropy is really the measure of how much energy ran for the hills before, during and after an event typically associated with heat.

Last modified: Friday, 3 March 2017, 4:35 AM