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The Basics of Organic Chemistry

Introduction

What is Organic Chemistry?

The word Organic is one of the most overused in the English language.

People use it as a derogatory term in phrases like Don’t eat that; it’s not organic. Of course, there is a precise scientific definition of the word. In science, Organic can be a biological or chemical term. In Biology it means any thing that is living or has lived. The opposite is Non-Organic. In Chemistry, an Organic compound is one containing Carbon atoms. The opposite term is Inorganic.

It’s the Chemical meaning I want to explore in this essay.

Molecules

All substances are made up of molecules which are collections of atoms. All the molecules in existence are made up of about a hundred different kinds of atoms.

For example, a water molecule is composed of two atoms of Hydrogen and one atom of Oxygen. We write its formula as H2O.

A molecule of Sulphuric Acid contains two atoms of Hydrogen, one atom of Sulphur and four atoms of Oxygen. Its formula is H2SO4.

These are simple molecules containing only a few atoms. Most Inorganic

molecules are small. Below are a few common inorganic substances with their formulas.

Name of Substance Formula

Carbon Dioxide CO2

Salt NaCl

Nitric Acid HNO3

Laughing Gas N2O

Ammonia NH3

Saltpetre (used in gunpowder) KNO3

Carbon Monoxide CO

Potassium Permanganate (used in labs) KMnO4

Calcium Carbonate (chalk) CaCO3

All of these molecules have less than a dozen atoms.

The symbols Ca, K, Mn, Na and Cl stand for calcium, potassium, manganese, sodium and chlorine.

Molecules With Carbon

Most atoms are only capable of forming small molecules. However one or two can form larger molecules.

By far and away the best atom for making large molecules with is Carbon. Carbon can make molecules that have tens, hundreds, thousands even millions of atoms! The huge number of possible combinations means that there are more Carbon compounds that those of all the other elements put together!

A single Carbon atom is capable of combining with up to four other atoms. We say it has a valency of 4. Sometimes a Carbon atom will combine with fewer atoms.

The Carbon atom is one of the few that will combine with itself.

In other words Carbon combines with other Carbon atoms.

This means that Carbon atoms can form chains and rings onto which other atoms can be attached.

This leads to a huge number of different compounds. Organic Chemistry is essentially the chemistry of Carbon

Carbon compounds are classified according to how the Carbon atoms are arranged and what other groups of atoms are attached.

Hydrocarbons

The simplest Organic compounds are made up of only Carbon and Hydrogen atoms only. Even these run into thousands! Compounds of Carbon and Hydrogen only are called Hydrocarbons.

Please note that the molecule structure images below show the structure of three dimensional molecules in two dimensional format.

Alkanes

The simplest Hydrocarbon is methane, CH4. This is the simplest member of a series of hydrocarbons. Each successive member of the series has one more Carbon atom than the preceeding member. This is shown in the table below.

As the reader can see, there is a series of these compounds with this general formula:

CnH2n+2

This series of compounds are called alkanes. The lighter ones are gases and used as fuels. The middle ones (7 Carbons to 12 Carbons) are liquids used in petrol (gasoline). The higher ones are waxy solids. Candle wax is a mixture of alkanes.

After Butane, the names of these compounds are from the Greek for the number of Carbon atoms followed by the suffix -ane. So, Decane would have the formula C10H22.

Polythene is a very large alkane with millions of atoms in a single molecule. Apart from being flammable, alkanes are stable compounds found underground.

In the alkanes, all four of the Carbon valency bonds are taken up with links to different atoms. These types of bonds are called single bonds and are generally stable and resistant to attack by other chemicals. Alkanes contain the maximum number of Hydrogen atoms possible. They are said to be saturated.

The alkanes are not the only hydrocarbons.

Alkenes

Another series of compounds is called the alkenes. These have a general formula:

CnH2n.

Alkenes have fewer hydrogen atoms than the alkanes. The extra valencies left over occur as double bonds between a pair of Carbon atoms. The double bonds are more reactive than single bonds making the alkenes chemically more reactive.

The simplest alkenes are listed in the table below:

These compounds are named in a similar manner to the alkanes except that the suffix is -ene.

Alkynes

A third series are the alkynes. These have the following formula: (CnH2n-2).

Alkynes have two carbon atoms joined by a tripple bond. This is highly reactive making these compounds unstable.

Examples of alkynes are:

These highly reactive substances have many industrial uses.

Again the naming of these compounds is similar to the alkanes except that the suffix is -yne.

Carbon Rings

Alkanes, alkenes and alkynes all contain Carbon atoms in linear chains.

There are also hydrocarbons arranged in rings. Some examples follow:

When rings are combined with chains, the number of hydrocarbons is virtually infinite.

And we are still using only two types of atoms (Carbon and Hydrogen). We will now add a third.

Carbon, Hydrogen and Oxygen

When Oxygen atoms are added, the variety of compounds grows enormously. In the table, each row discusses a series of compounds.

See this table in: In the examples each molecule has a single functional group.

It is possible to have two or more functional groups on a molecule. These can be the same group (as in Oxalic Acid — a poison found in rhubarb leaves — which has two fatty acid groups) or different (as in Hydroxymethanoic Acid — which has a hydroxyl group and a fatty acid group):

CH2OHCOOH : Hydroxymethanoic Acid

The most famous compounds containing Carbon, Hydrogen and Oxygen are the Carbohydrates. An example is the common sugar, Sucrose (C12H22O11).

This shows how varied and complex even simple organic compounds can be. Sucrose has a pair of rings: one hexaganol, the other pentaganol. Each ring contains an Oxygen atom. The rings are joined by an Oxygen (Ether) link. The entire compound contains several Hydroxyl (OH) groups.

Sucrose Isomerism

An interesting phenomenon with organic molecules is called isomerism. Let

us look at two compounds introduced earlier.

Dimethyl Ether: (CH3)2O and Ethanol: C2H5OH.

The first is a gas which will knock you out if inhaled. The second is common alcohol drunk in spirits. The two molecules are shown below.М

CH2OHCOOH : Hydroxymethanoic Acid

The most famous compounds containing Carbon, Hydrogen and Oxygen are the Carbohydrates. An example is the common sugar, Sucrose (C12H22O11).

This shows how varied and complex even simple organic compounds can be. Sucrose has a pair of rings: one hexaganol, the other pentaganol. Each ring contains an Oxygen atom. The rings are joined by an Oxygen (Ether) link. The entire compound contains several Hydroxyl (OH) groups.

Sucrose Isomerism

An interesting phenomenon with organic molecules is called isomerism. Let

us look at two compounds introduced earlier.

Dimethyl Ether: (CH3)2O and Ethanol: C2H5OH.

The first is a gas which will knock you out if inhaled. The second is common alcohol drunk in spirits. The two molecules are shown below.

Ethanol

Notice that both compounds contain 2 Carbon atoms, 6 Hydrogen atoms and 1 Oxygen atom.

Even though the atoms are the same, they are arranged differently. This yields two different compounds with the same number of atoms. These compounds are isomers and the phenomenon is called Isomerism.

In this example, the two molecules have different functional groups. They are structural isomers. Other types of isomers exist.

Isomerism increases the number of Organic compounds. The more Carbon atoms in a compound, the more ways of arranging the atoms and the larger number of isomers.

Adding Nitrogen

Many very important organic compounds contain Nitrogen. This produces more series of compounds.

See compounds in:

A famous compound containing Nitrogen is Trinitro Toluene (C6H2CH3(NO2)3 — usually abbreviated to TNT). This is an artificially made explosive. Its structure is shown below:

Trinitro Toluene (TNT)

There are six isomers of this compound as the three NO2 groups can be placed in six different arrangements on the ring. These are known as positional isomers.

Other Atoms

The vast majority of organic compounds contain Carbon, Hydrogen, Oxygen and Nitrogen. Other types of atoms can be included to form even more compounds. These can contain atoms like Phosphorus, Sulphur (e.g. Thiamine, Vitamin B1), Magnesium (e.g. Chlorophyll) and Iron (e.g. Haemoglobin).

As can be imagined, these additions increase the number of compounds.

Apart from the naturally occurring Organic compounds, millions more can be synthesised. These can include atoms like Chlorine (used in pesticides). Examples of organic compounds containing Chlorine are shown below.

There is no difference between the same substance extracted from living organisms and made in a laboratory.

I hope this introduction to Organic Chemistry indicates just how vast and interesting the subject is.

The study of organic chemistry — which focuses on carbon molecules — is central to all living organisms.

The ability to convert ingested fuel to usable energy is what differentiates a living organism from a dead one. The ingested fuel contains a variety of large molecules (macromolecules) that get broken down. When the macromolecules have been broken down into their smallest parts, they can enter the cells, which contain more macromolecules, which are involved in more processes.

The Basics of Organic Chemistry

What is organic chemistry?

In organic chemistry, the focus is on the element carbon. Carbon is central to all living organisms; however, thousands of nonliving things (such as drugs, plastics, and dyes) are made from carbon compounds. Diamonds are carbon atoms in a crystal structure. Diamonds are so hard because the atoms of carbon are so closely bonded together in the crystal form. That same ability to pack closely together makes carbon an excellent structural element in its other forms as well.

One atom of carbon can combine with up to four other atoms. Therefore, organic compounds usually are large and can have several atoms and molecules bonded together. Organic molecules can be large, and they comprise the structural components of living organisms: carbohydrates, proteins, nucleic acids, and lipids.

Carbon is key

In their outer shells, carbon atoms have four electrons that can bond with other atoms. When carbon is bonded to hydrogen (which is common in organic molecules), the carbon atom shares an electron with hydrogen, and hydrogen likewise shares an electron with carbon. Carbon-hydrogen molecules are referred to as hydrocarbons. Nitrogen, sulfur, and oxygen also are often joined to carbon in living organisms.

Long carbon chains = low reactivity

Large molecules form when carbon atoms are joined together in a straight line or in rings. The longer the carbon chain, the less chemically reactive the compound is. However, in biology, other measures of reactivity are used. One example is enzymatic activity, which refers to how much more quickly a certain molecule can allow a reaction to occur.

One key to knowing that a compound is less reactive is that its melting and boiling points are high. Generally, the lower a compound’s melting and boiling points, the more reactive it is. For example, the hydrocarbon methane, which is the primary component of natural gas, has just one carbon and four hydrogen atoms. Because it is the shortest carbon compound, it has the lowest boiling point (-162°C) and is a gas at room temperature. It is highly reactive.

On the other hand, a compound made of an extremely long carbon chain has a boiling point of 174°C (compared to water, which has a boiling point of 100°C). Because it takes so much more for it to boil, it is much less reactive and is not gaseous at room temperature.

Forming functional groups based on properties

In organic chemistry, molecules that have similar properties (whether they are chemical or physical properties) are grouped together. The reason they have similar properties is because they have similar groups of atoms; these groups of atoms are called functional groups.

Chemical properties involve one substance changing into another substance by reacting. An example of a chemical property is the ability of chlorine gas to react explosively when mixed with sodium. The chemical reaction creates a new substance, sodium chloride (table salt). Physical properties refer to different forms of a substance, but the substance remains the same; no chemical reaction or change to a new substance occurs.

Some of the properties that the functional groups provide include polarity and acidity. For example, the functional group called carboxyl (-COOH) is a weak acid. Polarity refers to one end of a molecule having a charge (polar), and the other end having no charge (nonpolar). For example, the plasma membrane has hydrophilic heads on the outside that are polar, and the hydrophobic tails (which are nonpolar) form the inside of the plasma membrane.

What Is the Role of Nucleic Acids in Living Things?

Nucleic acids are large molecules that carry tons of small details: all the genetic information. Nucleic acids are found in every living thing — plants, animals, bacteria, viruses, fungi — that uses and converts energy. Every single living thing has something in common.

People, animals, plants, and more all are connected by genetic material. Every living thing may look different and act different, but deep down — way deep down in the nucleus of cells — living things contain the same chemical«ingredients» making up very similar genetic material.

There are two types of nucleic acids: DNA (which stands for deoxyribonucleic acid) and RNA (which stands for ribonucleic acid). Nucleic acids are made up of strands of nucleotides, which are made up of a base containing nitrogen (called a nitrogenous base), a sugar that contains five-carbon molecules, and a phosphoric acid.deoxyribonucleic acid) and RNA (which stands for ribonucleic acid). Nucleic acids are made up of strands of nucleotides, which are made up of a base containing nitrogen (called a nitrogenous base), a sugar that contains five-carbon molecules, and a phosphoric acid.

Your entire genetic composition, personality, maybe even intelligence hinges on molecules containing a nitrogen compound, some sugar, and an acid. The nitrogenous bases are molecules either called purines or pyrimidines.

Purines include

  • Adenine
  • Guanine

Pyrimidines include

  • Cytosine
  • Thymine (in RNA)
  • Uracil (in DNA)

Deoxyribonucleic acid (DNA)

DNA contains two strands of nucleotides arranged in a way that makes it look like a twisted ladder (called a double helix). The nitrogenous bases that DNA builds its double-helix upon are adenine (A), guanine (G), cytosine (C), and thymine (T). The sugar that is in the composition of DNA is 2-deoxyribose.

Adenine is always paired with thymine (A-T), and guanine is always paired with cytosine (G-C). These bases are held together by hydrogen bonds, which form the «rungs» of the «twisted ladder.» The sides of the ladder are made up of the sugar and phosphate molecules.

Certain sections of nitrogenous bases along the strand of DNA form a gene. A gene is a unit that contains the genetic information or codes for a particular product and transmits hereditary information to the next generation.

But genes are not found only in reproductive cells. Every cell in an organism contains DNA (and therefore genes) because DNA also codes for the proteins that the organism produces. And proteins control cell function and provide structure. So, the basis of life happens in each and every cell.

Whenever a new cell is made in an organism, the genetic material is reproduced and put into the new cell. The new cell can then create proteins within itself and also pass on the genetic information to the next new cell.

The order of the nitrogenous bases on a strand of DNA (or in a section of the DNA that comprises a gene) determines which amino acid is produced. And the order that amino acids are strung together determines which protein is produced. Which protein is produced determines what structural element is produced within your body (such as, muscle tissue, skin, or hair) or what function can be performed (such as if hemoglobin is being produced to transport oxygen to all the cells).

Ribonucleic acid (RNA)

The nitrogenous bases that RNA uses are adenine, guanine, cytosine, and uracil (instead of thymine). And, the sugar in RNA is ribose (instead of 2deoxyribose). Those are the major differences between DNA and RNA.

In most animals, RNA is not the major genetic material. Many viruses — such as the human immunodeficiency virus (HIV) that causes AIDS — contain RNA as their genetic material. However, in animals, RNA works along with DNA to produce the proteins needed throughout the body.

For example, RNA has three major subtypes: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three of those subtypes are involved in protein synthesis

How Cell Substances Transport through the Plasma Membrane

The plasma membrane surrounding animal cells is where the exchange of substances inside and outside of cells takes place. Some substances need to move from the extracellular fluid outside cells to the inside of the cell, and some substances need to move from the inside of the cell to the extracellular fluid.

Some of the proteins that are stuck in the plasma membrane help to form openings (channels) in the membrane. Through these channels, some substances such as hormones or ions are allowed to pass through. They either are «recognized» by a receptor (a protein molecule) within the cell membrane, or they attach to a carrier molecule, which is allowed through the channels. Because the plasma membrane is choosy about what substances can pass through it, it is said to be selectively permeable.

Permeability describes the ease with which substances can pass through a border, such as a cell membrane. Permeable means that most substances can easily pass through the membrane. Impermeable means that substances cannot pass through the membrane. Selectively permeable or semipermeable means that only certain substances are able to pass through the membrane.

Transporting substances across the plasma membrane can require that the cell use some of its energy. If energy is used, the transport is called active. If molecules can pass through the plasma membrane without using energy, the molecules are using passive transport.

Helping the molecules across: Active transport

Sometimes, the molecules are just too big to easily flow across the plasma membranes or dissolve in the water so that they can be filtered through the membrane. In these cases, the cells must put out a little energy to help get molecules in or out of the cell.

Embedded in the plasma membrane are protein molecules, some of which form channels through which other molecules can pass. Some proteins act as carriers — that is, they are «paid» in energy to let a molecule attach to itself and then transport that molecule inside the cell.

Passive transport of molecules

A membrane can allow molecules to be passively transported through it in three ways: diffusion, osmosis, and filtration.

Diffusion: Sometimes organisms need to move molecules from an area

where they are highly concentrated to an area where the molecules are less concentrated. This transport is much more easily done than moving molecules from a low concentration to a high concentration. To go from a high concentration to a low concentration, in essence the molecules need to only

«spread» themselves, or diffuse, across the membrane separating the areas of concentration.

In the human body, this action occurs in the lungs. You breathe in air, and oxygen gets into the tiniest air sacs of the lungs, the alveoli. Surrounding the tiniest air sacs of the lungs are the tiniest blood vessels — capillaries. The capillaries in the lungs, called pulmonary capillaries, contain the lowest concentration of oxygen in the body, because by the time the blood gets to the tiniest vessels, most of the oxygen has been used up by other organs and tissues.

So, the tiniest air sacs of the lungs have a higher concentration of oxygen than do the capillaries. That means that the oxygen from the alveoli of the lungs can spread across the membrane between the air sac and the capillary, getting into the bloodstream.

Osmosis: This term is used when talking about water molecules diffusing across a membrane. Basically, the diffusion of water (osmosis) works as described in the preceding bullet. However, with osmosis, the concentration of substances in the water is taken into consideration. If a solution is isotonic, that means the concentrations of the substances (solutes) and water (solvent) on both sides of the membrane are equal. If one solution is hypotonic, there is a lower concentration of substances (and more water) in it when compared to another solution. If a solution is hypertonic, there is a higher concentration of substances in it (and less water) when compared to another solution.

For example, the blood in your body contains a certain amount of salt. The normal concentration is isotonic. If suddenly there is too high a concentration of salt, the blood becomes hypertonic (too many salt molecules). This excess of salt forces water out of the blood cells in an attempt to even things out. But the effect this action has is actually that of shrinking the blood cells.

This shrinking of cells is called crenation (not cremation). If too much fluid is in the bloodstream, the blood cells have too few molecules of salt in comparison, making them hypotonic. Then, the blood cells take in water in an attempt to normalize the blood and make it isotonic. However, if the blood cells need to take in too much water to bring everything back into balance, they can swell until they burst. This bursting of cells is called hemolysis (hemo = blood; lysis = break apart).

Filtration: The last form of passive transport is used most often in the capillaries. Capillaries are so thin (their membranes are only one cell thick) that

diffusion easily takes place through them. But remember that animals have a blood pressure. The pressure at which the blood flows through the capillaries is enough force to push water and small solutes that have dissolved in the water right through the capillary membrane. So, in essence, the capillary membrane acts as filter paper, allowing fluid to surround the body’s cells and keeping large molecules from getting into the tissue fluid.

Inorganic chemistry

What are acids? What are bases? How do they react together? What causes neutralization?

Acids and bases are fundamental chemicals in chemistry. In organic chemistry, the carboxylic acids have acidic properties, but in inorganic chemistry there is a wide range of acids with a variety of properties.

Definition of Acids and Bases

The word acid comes from the Latin word which means sour or sharp to the taste, and liquids like vinegar and lemon juice are well-known acids. Other properties of acids are that they are corrosive to some metals and turn a material called litmus, which is an indicator extracted from moss, red. Some common acids are citric acid — found in fruit juice, ethanoic acid — found in vinegar, sulfuric acid — found in car batteries, and carbonic acid, which is also known as soda water.

There are other chemicals which, when added to a mixture of acid and litmus, will turn it blue. These chemicals are called bases (alkalis when they are soluble) and their reaction with acid is called neutralisation. Common bases are calcium hydroxide (lime), sodium hydrogencarbonate (baking soda), magnesium hydroxide (milk of magnesia) and ammonia.

Acidity Depends on Hydrogen Ions

The behaviour of acids and bases is related to the presence of hydrogen ions (H+) in the solution. When an acid dissolves in water, it releases hydrogen ions, which cause the acidic properties. A strong acid, like sulfuric or hydrochloric acid, is an acid which is completely ionised in solution (Important: it has nothing to do with the concentration of the solution). A weak acid, like ethanoic or citric acid, is an acid which is not completely ionised.

The activity of a base is explained by its reaction with hydrogen ions. So, a base is able to react with hydrogen ions, reducing the acidic nature of the solution. Some bases are metal hydroxides, and the hydroxide part reacts with the hydrogen ion to make water. Other bases are carbonates or hydrogen carbonates which react with the hydrogen ions to make carbon dioxide and water. This explanation of how acids and bases work is called the BrønstedLowry definition of acids and bases, after the two scientists who first proposed it in 1923.

The pH Scale

A scale to demonstrate how acidic or basic a solution is has been developed, called the pH scale. It ranges from 1 to 14, in which the lowest numbers are for the most acidic and the higher numbers are the most alkaline, with pH 7 being neutral. The formula to work out the pH value is:

  • pH = -log [H+] where [H+] is the concentration of hydrogen ions in the solution. Some example of pH values:
  • pH1: stomach acid
  • pH3: vinegar
  • pH5: rainwater
  • pH7: pure water
  • pH9: baking soda
  • pH12: mineral lime
  • pH14:s odium hydroxide (Caustic Soda) Properties and Uses of the Alkaline Earth Metals Oct 2, 2010 Rochelle Joseph

Alkaline Earth Metals — Timothy Ismael (with permission)

The alkaline earth metals are the elements found in group two of the periodic table. The properties of these metals allow them to be classed together.

The metals which make up the group of alkaline earth metals are, from top to bottom, beryllium, magnesium, calcium, strontium, barium and radium.

Natural Occurrences Alkaline Earth Metals

Beryllium is only found combined with other elements in nature. Among its compounds are the gems: aquamarine, which is the turquoise variety of beryl; bixbite, also known as red beryl and emerald, which is green beryl. Beryllium is also a constituent of the gemstones chrysoberyl and phenacite. Beryllium is present in bertrandite, which is one of the main ores of beryllium.

Magnesium is found in over sixty minerals on earth. Among these, only dolomite, magnesite, brucite, carnallite, talc and olivine are of commercial importance.

Magnesium is the forth most abundant element in the earth’s crust where it constitutes only two per cent by mass. Magnesium is the eleventh most abundant element by mass in the human body, playing a major role in the manipulation of phosphate compounds such as ATP.

Magnesium is too reactive to occur naturally in is elementary state.

Calcium occurs naturally in sedimentary rocks such as calcite, dolomite and gypsum. Calcium can also be found in igneous rocks among which is plagioclase and in metamorphic rock such as garnets.

Calcium is a very abundant metal in the earth’s crust as well as the human body. Like the other Group Two metals, pure, uncombined calcium does not occur naturally because the metal is too reactive.

Read on

Strontium occurs mainly in the form of its carbonate and sulfate naturally. It is more commonly known to exist as a product of nuclear fall out.

Barium, like strontium occurs mainly in the form of its carbonate and sulfate.

Barium is also a constituent of the rare blue gemstone, benitoite.

Radium is a radioactive element. It is a decay product of uranium, and so, can be found in uranium ores.

Physical Properties of Alkaline Earth Metals

Alkaline earth metals are silvery, soft, low density metals which tarnish in air. They are so soft that they can be cut with a knife. Compared to other metals further in the periodic table, group two metals have low boiling and melting points. All alkaline earth metals have two valence electrons.

Alkaline earth metals burn in oxygen giving characteristic flames which are unique to each alkaline metal. Beryllium burns with a colorless flame, magnesium with a bright white flame and calcium with a brick red flame. Strontium burns with crimson flame while barium’s flame is colored apple green.

Major Uses of Alkaline Earth Metals

Beryllium

Beryllium is primarily used in alloys. Its low densities allows it to add strength to other metals without adding much weight. A very important alloy of beryllium is beryllium copper which is, as expected, a mixture of beryllium and copper, Beryllium copper is used to make tools which are to be used in hazardous environments. Its non-sparking and non magnetic properties allow this. Beryllium copper is also used in the production of some musical instruments such as the tambourine and triangle. Furthermore, Beryllium copper is used in the production of bullets, precision measurement devices and in aerospace.

Magnesium

Like beryllium, magnesium is also used in alloys because it lends strength without adding much weight. Duralumin, an alloy of magnesium, aluminum and copper, is used in the production of air crafts and small boats. Other magnesium alloys are used in the production of household material.

Magnesium is used as flares and distress signals. This use is attributed to the bright white light produced when burning magnesium in oxygen.

Magnesium compounds are also very useful. These include magnesium oxide which is used as a refractory lining material, magnesium sulfate which is used as epson salts, as artificial snow and in fertilizers and magnesium hydroxide which is used as an antacid.

Calcium

Calcium’s usefulness is found mainly in its compounds. However, calcium in its elemental form is used in alloys and as a de-oxidizer in steel.

Calcium compounds are especially important to a healthy body. They are involved in the strengthening of bones and teeth and in the transfer of nerve impulses. Calcium compounds are also involved in the control of fertilization in the human body permitting only one sperm to enter the egg.

Plaster of Paris which is used in casts is made of calcium sulfate. Gypsum wallboard, often called plasterboard, is also made of calcium sulfate.

Calcium carbonate, which exists as limestone, chalk, and marble is very important in the construction industry.

Barium

Barium is used in alloys with calcium and lead. Barium sulfate is used in medicine as a ‘barium meal’. Patients swallow the sulfate which is relatively opaque to X-Rays and shows particularly well on X-Ray photographs.

Group Two metals, called the alkaline earth metals, have similar properties which allow them to be grouped together. These metals are very useful both in their elemental form and in compounds.

The Chemistry, Properties and Uses of Hydrogen Apr 9, 2010 Simon Davies

Hydrogen Rocket Fuel — Mike Gieson

Hydrogen is the smallest, lightest, most abundant element in the universe, and the foundation of the Hydrogen Economy.

The element hydrogen is believed to be the most abundant element in the universe. It is the first element in the Periodic Table, containing just one proton in its nucleus. As an element, hydrogen exists as a diatomic molecule: H2 and is a gas at standard temperature and pressure.

Properties of Hydrogen

Hydrogen is a colourless, odourless, flammable gas. It is also much lighter than air, so a large proportion of elemental hydrogen produced on earth is lost from the atmosphere. Hydrogen has three common isotopes: Protium has one proton and no neutrons in its nucleus, so it has a mass number of 1; it makes up 99.985% of all hydrogen. Deuterium (D) has one proton and one neutron in its nucleus, and is sometimes called ‘heavy hydrogen’. Tritium has one proton and two neutrons in its nucleus, and is a radioactive isotope.

Compounds of Hydrogen

On earth, hydrogen is the third most abundant element in terms of number of atoms (behind oxygen and silicon), but ninth in terms of mass. Virtually all of this hydrogen is found combined in molecules, the most abundant being water (H2O). Hydrogen forms a large number of other compounds, however, being assigned an oxidation number of +1 or -1 depending on the electronegativity of the element to which it is bound.

Covalent Hydrogen Compounds

In its +1 oxidation state, hydrogen is found in binary compounds such as hydrogen chloride (HCl), hydrogen sulphide (H2S), and ammonia (NH3) in which it is covalently bonded to a more electronegative atom. Other compounds of hydrogen include acids like sulphuric acid (H2SO4) and nitric acid (HNO3); basic hydroxides like sodium hydroxide (NaOH) and calcium hydroxide (Ca(OH)2); and acid salts like sodium hydrogen phosphate (NaH2PO4) and sodium hydrogen carbonate (NaHCO3). Additionally it is present in many organic compounds, covalently bonded to carbon (CH4, C2H6 etc).

Metal Hydrides

In its -1 oxidation state, hydrogen is found in compounds with metals, called hydrides. These are ionic when hydrogen is combined with alkali or alkalineearth metals like sodium or potassium. It also forms covalent bonds with elements silicon and antimony. With transition metals, lathanides or actinides, the hydrogen seems to dissolve into the structure of the metal, giving a more brittle substance which is still a conductor or semiconductor.

Uses of Hydrogen

Large quantities of hydrogen are used in the Haber Process, which turns nitrogen from the air into ammonia used in fertilizers. It is also used in the hydrogenation of fats and oils, the production of methanol, hydrocracking and metal refining. It is also an important rocket fuel, used by NASA to launch the space shuttles. Deuterium is used in nuclear power stations as a moderator to slow neutrons down.

Read on

The Hydrogen Economy

The potential of hydrogen as a clean source of energy has led many people to talk about a ‘hydrogen economy’ to replace the present, hydrocarbon-based economy. Cars powered by fuel cells which use the energy stored in hydrogen, and only emitting water vapour are regularly promised, but unfortunately the technology has a long way to go. The main problem is the energy needed to produce the hydrogen — either from water, or from hydrocarbons themselves, which seems to defeat the object.

Preparation of Soluble Metal Salts in the Lab

Reactions Between Acids and Metals or Bases Makes Ionic Compounds Jan 11, 2010 Adrienne Larocque

Adding iron filings to test tube with acid — Photo by Adrienne Larocque

An acidic solution can be neutralized by reacting it with a base, a metal or a carbonate. The products of these neutralization reactions are called salts.

Salt, also known as sodium chloride, is a dietary mineral. Salts, on the other hand, are ionic compounds consisting of a metal cation (positively-charged ion) bonded to a simple or polyatomic anion (negatively-charged ion). High school chemistry courses typically require students to prepare metal salts in the laboratory by mixing various dilute acids with bases or certain metals.

An acid may be defined as any substance that dissociates and donates a hydrogen ion (H+) to a base. A base may be defined as any substance that contains a hydroxide ion (OH-) or produces it in solution (by reacting with water, for example). Not all bases are soluble in water; those that are soluble are called alkalis.

Laboratory Methods for Preparing Soluble Metal Salts

In high school laboratory settings, dilute acids should be used to ensure student safety. There are 4 standard methods for the preparation of metal salts:

  • Mixing an acid with a base
  • Mixing an acid with a metal
  • Mixing an acid with a metal oxide
  • Mixing an acid with a carbonate

Because the salts are soluble, it is necessary to gently heat the resultant solution to drive off the water. Eventually, the solution will become saturated and the metal salt will crystallize.

Reaction of an Acid with a Base

Sodium hydroxide (NaOH) is an example of an alkali, that is, a soluble base. Combining an aqueous solution of sodium hydroxide with dilute hydrochloric acid neutralizes the acid:

HCl(aq) + NaOH(aq) --> NaCl(aq) + H2O(l)

The hydrogen ion from the acid combines with the hydroxide ion from the base to produce water, and the cation from the base combines with the anion from the acid to produce the salt. The reaction seems unremarkable as the production of gas bubbles observed in some of the following reactions does not occur here. Students may observe some small degree of immiscibility, apparent as «squiggly» lines in the solution. The product of the reaction of this strong acid and strong base is simple salt water.

Reaction of an Acid with a Metal

In school laboratories it is necessary to use less reactive metals such as magnesium (Mg), aluminum (Al), zinc (Zn), iron (Fe) and tin (Sn) as a safety precaution. As an example, consider the addition of iron filings to a test tube containing sulfuric acid. The reaction equation can be written as follows:

H2SO4(aq) + Fe(s) --> FeSO4(aq) + H2(g)

Bubbles of hydrogen gas will be observed as the reaction proceeds. The test to confirm that hydrogen is produced is to place a lit splint near the mouth of the test tube. A popping sound will be heard.

Reaction of an Acid with a Metal Oxide

Metal oxides also are bases. They may be soluble or insoluble, depending on the cation species. Water-soluble oxides (oxides of alkali and alkaline earth metals) form metal hydroxides in solution. Oxides of transition metals generally are insoluble. Consider the following reaction between insoluble copper oxide and sulfuric acid:

H2SO4(aq) + CuO(s) --> CuSO4(aq) + H2O(l)

The reactant copper oxide will slowly dissolve in the acid. Because the product copper sulphate is dissolved, the solution will have a characteristic blue colour.

Reaction of an Acid with a Carbonate

Carbonates are also considered to be bases, even though they do not contain OHgroups. In any case, the reaction between an acid and a carbonate produces an obvious reaction in which carbon dioxide (CO2) gas is produced. For example:

2HCl(aq) + CaCO3(s) --> CaCl2(aq) + CO2(g) + H2O(l)

The test for CO2 involves bubbling the unknown gas through limewater (a saturated solution of calcium hydroxide). If the solution turns milky, the gas is carbon dioxide.

Summary of Acid-Neutralizing Reactions

To summarize, there are 4 standard reactions that neutralize acids and produce metal salts:

  • Acid + base --> a salt + water
  • Acid + metal --> a salt + hydrogen gas
  • Acid + metal oxide --> a salt + water
  • Acid + carbonate --> a salt + carbon dioxide gas + water

The common factor amongst these reactions is that they all produce a salt dissolved in water. Two of the reactions also produce gas which bubbles out of the solution

African Journal of Pure and Applied Chemistry Vol. 4(9), pp. 177-182, October 2010

The ground state structure and properties of erythritol in gas phase and in different solvents: A DFT / SC-IPCM approach

D. De, S. Dalai and B. R. De*

Department of Chemistry and Chemical Technology, Vidyasagar University, Midnapore-721102, West Bengal, India. Accepted 27 July, 2010

Abstract

Quantum mechanical study of the ground state structure and properties of erythritol was carried out in gas phase and in different solvents at the hybrid B3LYP DFT level with complete geometry optimization and varying basis sets [6-311G (d,p) and 6-311++G (d,p)] in order to provide detailed information of the model molecule in solvents of low, medium and high dielectric constant. It was found that the molecule is stabilized by solvation in all cases, the order of stability being water > DMSO > carbontetrachloride.

The dipole moment was increased. The charge density on O-atoms were increased almost as per above order indicating that there are two types of O-H groups in the molecule in agreement with the reported experimental findings. Carbon skeleton were planar in water and DMSO by 6-311++G (d,p) basis set gave non planar structure in CCl4. The geometries in water and DMSO were in excellent agreement with the experiment. The calculated IR frequencies are well when compared with the experimental results. The HOMO-LUMO gap remained almost same on solvation.

Key words: B3LYP DFT, GAUSSIAN, erythritol, charge distribution, gas phase.

INTRODUCTION

The rapid development of both theory and software makes it possible to have detailed studies of the structure and properties of different molecules in gas phase and in solution. There is a growing interest in the study of important biomolecules both theoretically (Ladik, 2004) and experimentally. Among the biomolecules, carbohydrates are very important as they coordinate with various metal ions like Cu+2, Mn+2, Fe+2, Zn+2 etc. in playing vital role in versatile metabolic activities. Why these metal ions do so is to be answered. Carbohydrate research is a challenging field and its progress is much slower experimentally.

Recently, single crystals of co-ordinated complexes of neutral erythritol (C4H10O4) with various metal ions were synthesized and studied using FT-IR and single crystal X-ray diffraction analysis (Yang et al., 2004a and b). There are several theoretical (gas phase and water phase) and experimental reports (Jesus et al., 2005a and b; 2006; Ceccarelli et al., 1980; Shimada et al., 1959; Hao et al.,

*Corresponding author. E-mail: 2005) on the erithritol molecule. In reference to Jesus et al. (2005a), a detailed study of the molecule has been done in gas phase using DFT method using 6-311++G (d,p) basis set and in reference to Jesus et al. (2005b), enthalpy of sublimation of erythritol in solid state has been determined and some terms have been calculated in gas phase by DFT method using 6-311++G(d,p) basis set. In reference to Jesus et al. (2006), a beautiful study of the same molecule in water phase has been done using CPCM model. Ceccarelli et al. (1980) and Shimada et al. (1959) have reported the crystal structure of the erythritol molecule been and Hao et al. (2005) has reported the solubility of erythritol in different solvents and solvent mixture (water, methanol, ethanol, acetone). Structure and properties of erythritol in its ground state and first excited state in gas phase without the solvent effects have been reported theoretically using lower basis set (De et al., 2006). In the present work, we have undertaken the detailed systematic and comprehensive theoretical investigation on the structure and properties of the simplest representative of the carbohydrates, that is erythritol in its ground state both in gas phase and in different solvents of low, medium and high dielectric constant by the hybrid B3LYP DFT method (Gaussian 03W Program,(Gaussian, Inc., Wallingford, CT) 2004; Lee, 1988; Becke et al., 1993) using [6-311G (d,p) and 6-311++G (d,p)] basis set in order to have detailed information about the model molecule because the higher basis sets are more reliable in this respect. This theory (DFT) has recently become popular in quantum chemistry because present day approximate functionals provide a useful balance between accuracy and computational cost, allowing much larger systems to be treated than traditional ab initio methods, retaining much of their accuracy. This theory is the way of approaching any interacting problem, by mapping it exactly to a much easier-to-solve non-interacting problem using higher basis set. Three solvents [carbon tetrachloride ( = 2.228), DMSO ( = 46.7) and water ( = 78.39)] were chosen as the case study.

COMPUTATIONAL DETAILS

Complete geometry optimizations for the ground state in the gas phase were carried out with B3LYP DFT method with 6-311G (d,p) and 6-311++G (d,p) basis sets using GAUSSIAN 03W program (Gaussian 03W Program,(Gaussian, Inc., Wallingford, CT) 2004; Lee, 1988; Becke et al., 1993). In case of solution the optimized energies were computed using the SCIPCM SCRF model and B3LYP DFT method with the same basis set. The iso-density PCM (IPCM) model defines the cavity as an iso-density surface of the molecule. This isodensity is determined by an iterative process in which an SCF cycle is performed and converged using the current iso-density cavity. The resultant wave function is then used to compute an updated iso-density surface, and the cycle is repeated until the cavity shape no longer changes upon completion of the SCF.

An iso-density surface is a very natural, intuitive shape for the cavity since it corresponds to the reactive shape of the molecule to as great a degree as is possible (Rather than being a simpler, pre-defined shape such as a sphere or a set of overlapping spheres).

However, a cavity defined as an iso-surface and the electron density are necessarily coupled. The Self-consistent iso-density Polarized Continuum Model (SCI-PCM) was designed to take this effect fully into account. It includes the effect of solvation in the solution of the SCF problem. This procedure solves the electron density which minimizes the energy, including the solvation energydensity. In other words, the effects of solvation are folded into the iterative SCF computation rather than comprising an extra step afterwards. SCI-PCM thus accounts for the full coupling between the cavity and the electron density and includes coupling terms that IPCM neglects.

In the frequency calculation we specified, scf = tight, criteria and the basis set is 6-311G (d,p) only for all the solvents, because of computation time problem.

RESULTS AND DISCUSSION

Calculated equilibrium geometry of erythritol in its ground state both in gas phase and in different solvents are given in Table 1 along with the numbering scheme of the atoms of the molecule. Some important properties of the molecule are listed in Table 2. Mulliken atom electron density is recorded in Table 3. Atomic charge is not an observable quantum mechanical property. All methods for computing the atomic charges are necessarily arbitrary. Electron density among the atoms in a molecular system is being partitioned. Mulliken population analysis computes charges by dividing orbital overlap equally between the two atoms involved. Therefore the values are non-unique and depend on the basis set used.

Still, it is widely used. Figures 1 to 8 show the three dimensional structure of erythritol molecule with atom numbering at the calculated equilibrium geometry in gas phase, water, DMSO and carbon tetrachloride respectively. The significance of the figures is that it shows the complete three dimensional structures which are not completely reflected from the selected geometrical parameters given in the table. From Table 1, it is seen that the geometrical parameters do not change significantly between the basis sets but the chemical properties change a lot.

In the gas phase the torsion angle, C1-C4-C5-C6 of the molecule calculated by both basis sets shows non planarity of the carbon skeleton as expected. In water and DMSO this angle comes out to be 173.9 and -174.6 respectively only by 6-311++G (d,p) basis set calculation showing planarity of the carbon skeleton supporting the chemical expectations whereas the other results show non planarity. In carbon tetrachloride, the skeleton remains non planar as in the gas phase indicating that solvent polarity has marked influence on the structure of the molecule.

This is further revealed in other results of torsion angles like O-C-C-O, C-CC-O where the experimental results are well reproduced in water and DMSO but not in carbon tetrachloride. Regarding the C-O and C-C distances, they are in excellent agreement with the experimental results [7, 8, and 12] in all calculations and in all solvents. The same is true for the C-C-H, C-C-O and C-CC angles. From Table 2 it is clear that the molecule is stabilized in all solvents by all calculations because of the less nuclear repulsion in each case. The solvation energy is of the order water > DMSO > carbon tetrachloride as obvious from chemical expectation arising out of the dielectric constant of the solvents. The dipole moment is increased in all solvents indicating that the charge separation is higher in the solution as is expected for a polar molecule. This is supported by the data from Table 3 where it is seen that the charge density on Oatoms are much more increased than that in the gas phase. Among the four oxygen atoms in the molecule the O13 carries the highest negative charge in all calculations and in all solvents with the exception of water by 6-311G (d, p). This indicates that O13-H18 group may behave differently from the other three O-H groups of the molecule showing that the molecule can behave as a bidentate ligand. This is in excellent agreement with the experimental findings (Yang et al. 2004a and b). From Table 3 it is also seen that all the carbon atoms are negatively charged both in gas phase and in solvated phase by 6-311++G (d, p) set as expected by electro-negativity rule whereas 6-311G (d, p) set shows C1 to be negatively charged both in gas phase and in solution phase and C5 to be negatively charged in solution phase with the exception of DMSO where it is positively charged which is unusual according to the electro negativity rule.

The H-atoms attached to O-atoms contain almost equivalent positive charges whereas those attached to C-atoms are less positively charged than the former both in gas phase and in solution phase and in all calculations as expected from the general electro negativity rule. The HOMO-LUMO gap increases on solvation and remains almost equivalent in all solvents. The calculated O-H frequencies using a scale factor 0.8439 is generated in the present study. In Yang et al. (2004a), the IR spectra were measured on a Nico-plan IR microscope attached on a Nicolet Magna-IR 750 FT-IR spectrometer. Four O-H vibrations have beencomputed to see whether there is any difference between them. The results show that there are two types of O-H frequencies.

The results are well compared with theexperimental findings (Yang et al., 2004a). The O13-H18 frequency is highest among the four O-H bonds both in gas and solution phase. The value is little decreased from the gas phase value in water and in DMSO, but remains almost same in carbon tetrachloride as expected from the solvent polarity point of view.

Conclusion

From the present study it can be concluded that neutral erythritol can coordinate with various transition metal ions through O-H groups in the ground state both in gas and solution phase, the complexation being better in solvents of higher dielectric constants. The two types of O-H groups confirm that the molecule may behave as a bidentate ligand in excellent agreement with the experimental findings (Yang et al., 2004a and b). B3LYP DFT 6-311++G (d, p) results are more reliable in the present study.

ACKNOWLEDGEMENTS

We gratefully acknowledge the support of UGC and DST, New Delhi.

REFERENCES

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