Chemistry of covalent bonds. Unit 2: SMELLS Molecular Structure and Properties

Chemistry of covalent bonds Unit 2: SMELLS Molecular Structure and Properties

How do elements combine that have similar electronegativities?

Property of almost all elements the ability to combine with other elements and form compounds* Combine in fixed ratios. Hydrogen peroxide Glucose C 6 H 12 O 6 *the combination of two or more different kinds of atoms.

In a compound, the different elements lose their individual chemical properties.

Compounds and Chemical Formula Compounds often have common names such as water or salt - but are also named by their formula which tell what elements make up the compound and in what proportion. For example, a molecule of water is made up of two hydrogen atoms for every one oxygen atom. H 2 O

Law of conservation of mass Mass is not created or destroyed during a chemical reaction or physical change but it can change form.

Compounds can be separated based on their size and charge.

The reactions/actions of elements that share electrons

How compounds form -

Electron arrangement determines the chemical properties of an atom

e - move around the nucleus in specific energy levels

Each energy level (shell) is numbered starting closest to the nucleus. This is called the energy level s quantum number Max. # of e- in each energy level calculated by the formula: 2n 2 (where n is the quantum number)

Each atomic orbital and the electrons in it are associated with a specific amount of energy, and the farther an electron is from the nucleus the greater its energy (very important).

*The electrons in the outermost (highest) E level.

It is the outermost electrons that determine the chemical properties of the element. (very important)

These outermost electrons are the one s that are involved in bonding. Chemistry of an element depends almost entirely on the number of its valence electrons.

Chemical Bonding A chemical bond results from strong electrostatic interactions between two atoms. The nature of the atoms determines the kind of bond. Atoms bond to achieve stability reach a stable OCTET

Predicting types of bonds How do you predict what type of bond will from between atoms? Notice the location of the elements in the Periodic Table. As a rule, elements on the right (non-metals) share electrons with each other (covalent bonds) and elements on the left tend to donate electrons to elements on the right (ionic bonds).

What factors determine if an atom forms a covalent or ionic bond with another atom? The number of electrons in an atom, particularly the number of the electrons furthest away from the nucleus determines the atom s reactivity and hence its tendency to form covalent or ionic bonds.

Ionic Bonding If enough energy is applied, either by another element or by external photons, electrons can be pushed so far that they escape the attraction of the nucleus Losing an electron is called ionization

Losing/gaining an electron is called ionization An ion is an atom that has either a net positive or net negative charge.

cation

It is possible that, as two atoms come close, one electron is transferred to the other atom. The atom that gives up an electron acquires a +1 charge and the other atom, which accepts the electron acquires a 1 charge. The two atoms are attracted to each (opposite charges attract) resulting in an IONIC bond.

3 Biologically Important Properties of Ionic Compounds Ionic compounds are soluble in water.

In aqueous solution, an ionic compound dissociates into its ions.

The dissociated ions in aqueous solution give the solution the ability to conduct electricity.

Metallic Bonds Metallic bonds occur when metal atoms share electrons. Electrons in the outer shells float together loosely and form a sea electrons.

This also explains why metals are good conductors

Metallic bonding The outer electrons are so weakly bound to metal atoms that they are free to roam across the entire metal. Having lost their outer electrons, individual metal atoms are more like positive ions in a swarm of communal electrons.

Lesson 1: Sniffing Around Molecular Formulas What does chemistry have to do with smell? Smell appears to be related to molecular formula and chemical name.

Lesson 2: Molecules in Two Dimensions Structural Formulas

Key Question How can molecules with the same molecular formula be different? You will be able to: describe the difference between structural formulas and molecular formulas recognize isomers

Molecular formula: The chemical formula of a molecular substance, showing the types of atoms in each molecule and the ratios of those atoms to one another.

Covalent Bonds A chemical bond that involves sharing a pair of electrons between neutral atoms in a molecule in order to achieve an octet in the valence shell. In covalent bonding the attraction for electrons is similar for two atoms.

COVALENT bonds result from a strong interaction between NEUTRAL atoms Each atom donates an electron resulting in a pair of electrons that are SHARED between the two atoms

For example, consider a hydrogen molecule, H 2. When the two hydrogen, H, atoms are far apart from each other they are not attracted to each other. As they come closer each feels the presence of the other. The electron on each H atom occupies a volume that covers both H atoms and a COVALENT bond is formed. Once the bond has been formed, the two electrons are shared by BOTH H atoms.

COVALENT bonds result from a strong interaction between atoms of similar electronegativity and electron affinity. Each atom donates an electron resulting in a pair of electrons that are SHARED between the two atoms

Generally, elements with similar electronegativity form covalent bonds

Atoms can bond forming single, double, triple and even quadruple covalent bonds. ethene

O Structural formulas indicate kind, number and arrangement of bonds using a line to represent a shared e- pair H H

One word of warning: hydrogen behaves with a divided personality. While it is traditionally placed in the periodic table above lithium, and can form ions (as in the case of acids), it typically forms covalent bonds. And remember: As with all generalizations, there are exceptions.

3 Biologically Important Properties of Covalent Compounds

Because the angles formed between covalently bonded atoms are specific and defined - biological molecules formed with covalent bonds have definite and predicable shapes. glucose

matter Anything that has mass and takes up space.

Bond energy. A covalent bond STORES energy so breaking those bonds releases energy that can be used for the needs of living organisms. Covalent bonds represent chemical potential energy that can be used in biological reactions. An example of this are the phosphoanhyride bonds of ATP.

Polarity polar covalent bonds are extremely important because of the unique properties exhibited by molecules with these kinds of bonds. (this is particularly true for living organisms)

The structure of covalent molecules: Structural Formulas

remember Structural formulas indicate kind, number and arrangement of bonds using a line to represent a shared e- pair

Drawing structural formulas First identify the valence electrons. Draw Lewis dot structures Apply the octet rule to determine where and how many bonds will form. Replace shared electrons with line. Leave dots for lone pairs of electrons Represent the correct geometry.

Lone pair: A pair of valence electrons not involved in bonding within a molecule. The two electrons belong to one atom. After bonding, each atom has a total of eight valence electrons surrounding it. (H exception) Bonded pair: A pair of electrons that are shared in a covalent bond between two atoms.

Draw the Lewis dot structure for the two covalently bonded molecules shown here. Explain how you arrived at your answer. a. O 2 b. NH 3 Draw the molecular structure for the two covalently bonded molecules shown here. Explain how you arrived at your answer.

from the text: The HONC 1234 rule and the octet rule both help you figure out Lewis dot structures and structural formulas. Both the HONC 1234 rule and the octet rule can be satisfied by using double and triple bonds appropriately. It is not possible to create a triple-bonded oxygen compound, according to the HONC rule. There are exceptions to the bonding rules laid out here.

A Puzzling Activity Each puzzle piece contains the correct number of valence electrons for that atom. It also contains the appropriate number of tabs for bonding.

Structural formulas show how the atoms in a molecule are connected. A molecular formula can be associated with more than one structural formula.

Isomers The structural formula for certain molecules can differ. Compounds with the same molecular formula but different structural formulas are isomers.

C4H8O2

chemical compounds which have a common chemical formula, but not a common structure. This gives isomers different chemical properties

structural isomers C 5 H 12 show a different arrangement in covalent bonds Usually occur in differences in the arrangements of the carbon skeleton. Locations of double bonds may vary also

Differ in covalent arrangement OR location of double bond

Geometric isomer cis-2-butene trans-2-butene differences in arrangements of atoms around a double bond. (double-bonded carbons do not exhibit rotation). When molecules/functional groups are found on the same side of a double bond, this is known as the "Cis" configuration When atoms/functional groups are located on opposite sides of a double bond, this is called the "trans" configuration

Example in the biological world This is a schematic diagram of a rod cell. The stacked disks contain rhodopsin, the complex of opsin protein and 11-cisretinal. The nerve fires a signal to the brain as a result of retinal isomerization passed along to a connecting nerve cell, creating an electrical impulse interpreted as visual information by the brain.

Upon absorption of a photon in the visible range, 11-cis-retinal can isomerize to alltrans-retinal. Note how the size and shape of the molecule change as a result of this isomerization.

optical isomers when 4 different atoms/functional groups occur around a single carbon This results in molecules which are "mirror images" of each other, but NOT IDENTICAL. The resulting molecules do not function the same.

Amino acids & proteins often show this feature. Biological systems usually can identify and use the correct form, the other is usually ignored.

dextro = right levo = left The two forms of an enantiomer are known as the "L" form or the "D" form

Example in the biological world Thalidomide Laboratory tests after the thalidomide disaster showed that the 'S' enantiomer was teratogenic but the 'R' isomer was an effective sedative. It is now known that even when a selective sample of thalidomide is created, it can cause racemizing. This means that both enantiomers are formed in a roughly equal mix in the blood. So, even if a drug of only the 'R' isomer had been created, the disaster would not have been averted.

phocomelia

polarity Electron position in a covalently bonded molecule

Polar covalent bonds Polar covalent bonds are a particular type of covalent bond. In a polar covalent bond, the electrons shared by the atoms spend a greater amount of time, on the average, closer to one nucleus (in this example- Oxygen) than the other nucleus (in this case Hydrogen). This is because of the geometry of the molecule and the great electronegativity difference between the two atoms.

Consider, carbon (C) and chlorine (Cl). Chlorine is clearly to the right of carbon. Carbon is however fairly central. Electrons in a bond between these two elements are shared (covalent), but they are not shared equally. The shared electrons (one from Cl, one from C) would spend more of their time under the influence of chlorine, being farther right, but are not completely lost to carbon (as they would be to sodium).

The electrons being shared are held closer to the Cl than to the C giving the molecules slightly charged areas.

In a polar covalent bond, the electrons shared by the atoms spend a greater amount of time, on average, closer to one of the nucleus of one of the atoms. This is because of the geometry of the molecule and the great electronegativity difference between the two atoms.

The result of this pattern of unequal electron association is a charge separation in the molecule, where one part of the molecule has a partial negative charge and the other has a partial positive charge. (You should note this molecule is not an ion because there is no exchange of electrons, but there is a simple charge separation in this electrically neutral molecule.)

Polar covalent bonds are extremely important in biological systems because they allow the molecules to form another kind of weak bond.

The biological importance of polar covalent bonds is that these kinds of bonds can lead to the formation of a weak bond called a hydrogen bond.

Hydrogen bonds How are they formed? a hydrogen bond is formed when a charged part of a molecule having polar covalent bonds forms an electrostatic (as in positive attracted to negative) interaction with a substance of opposite charge. Molecules that have nonpolar covalent bonds do not form hydrogen bonds. Important. Hydrogen bonds are extremely important in biological systems. Their presence explains many of the properties of water. They are used to stabilize and determine the structure of large macromolecules like proteins and nucleic acids. They are involved in the mechanism of enzyme catalysis.

Strength. Hydrogen bonds are classified as weak bonds because they are easily and rapidly formed and broken under normal biological conditions. What classes of compounds can form hydrogen bonds? Under the right environmental conditions, any compound that has polar covalent bonds can form hydrogen bonds.

Polar/nonpolar lab

Water Water is the most abundant molecule in the body. Water forms the internal ocean that baths every cell of the human body. It makes up around 65% of the body weight. The water molecule is composed of one atom of oxygen and two atoms of hydrogen held together by covalent bonds. The polarity of water plays a critical role in all living and nonliving systems

The shape of the water molecule and the atoms in it give water a special property called polarity. This means that one end of the molecule is slightly positive while the other end is slightly negative.

Special properties of water Water exhibits some very special and unique properties that make it a critical compound.

Special Properties of Water. Polar: H bonding, adhesion and cohesion. High specific heat. Universal Solvent. High Surface Tension. Has capillary action.

Polarity properties Polarity gives water several special properties that are very useful for living organisms : COHESION ADHESION HYDROGEN BONDING

Universal Solvent In a solution one or more substances are dissolved. The dissolved substances are called solutes. The water which dissolves the solutes is called the solvent. Water is so effective at dissolving substances that it is referred to as the universal solvent. Notice how the negative ends of water attract sodium and the positive ends attract chloride.

hydrogen bond They are simply a special type of powerful dipoledipole attraction. Water is an example of a molecule that has polar covalent bonds and engages in hydrogen bonding.

Hydrogen bonds are caused by dipole attraction between two molecules containing hydrogen bonded to small electronegative elements (N, O or F).

Hydrogen Bonding The dipole forces are attracted. A low-energy bond forms. This attractive force is what gives water its cohesive and adhesive properties. Molecules that have nonpolar covalent bonds form hydrogen bonds.

Cohesion Water attracted to other water. This is caused by hydrogen bonds that form between the slightly positive and negative ends of neighboring molecules. This is the reason why water is found in drops; perfect spheres.

Surface Tension Surface tension is the name we give to the cohesion of water molecules at the surface of a body of water. Water Strider

Can You Float A Paper Clip? water has the ability to support small objects. The hydrogen bonds between neighboring molecules cause a film to develop at the surface.

Breaking The Surface Tension What happened when you added a drop of detergent? Why? The detergent has phosphate in it. The phosphate attracts to the water molecules and breaks the surface tension.

adhesion Water can also be attracted to other materials. This is called adhesion. (Remember adhesive tape picks up things)

What do you observe when you placed a drop of water onto a piece of wax paper? Why do you think it is this shape?

007 Science You only Live Twice

What is happening?! Water is not attracted to wax paper (there is no adhesion between the drop and the wax paper). Each molecule in the water drop is attracted to the other water molecules in the drop. This causes the water to pull itself into a shape with the smallest amount of surface area, a bead (sphere). All the water molecules on the surface of the bead are 'holding' each other together or creating surface tension.

Capillary Action Capillary action is related to the adhesive properties of water. Capillary action is when water moves up a cylinder.

What is happening with the straw demonstration? the water molecules are attracted to the straw molecules. When one water molecule moves closer to the straw molecules the other water molecules (which are cohesively attracted to that water molecule) also move up into the straw.

Capillary action is limited by gravity and the size of the straw. The thinner the straw or tube the higher up capillary action will pull the water. This explains how a meniscus forms in a cylander.

Apply these properties to answer WHY the meniscus is different. glass plastic (wax)

Plants and Capillary Action Plants take advantage of capillary action to pull water from the soil into themselves. From the roots water is drawn through the plant by another force, transpiration.

Specific Heat Water has a high heat capacity. Specific heat (a measure of heat capacity), is the heat required to raise the temperature of 1 gram of water 1 C. Water, with its high heat capacity, changes temperature more slowly than other compounds that gain or lose energy.

Water As a Habitat Water s resistance to sudden changes in temperature makes it an excellent habitat (organisms adapted to narrow temperature ranges may die if the temperature fluctuates widely). The heat retaining properties of water provide a much more stable environment than is found in terrestrial situations. AND Fluctuations in water temperature occur very gradually (seasonal extremes are small).

Hydrogen bonds are extremely important in living systems Hydrogen bonds are responsible for the unique properties of water and they loosely pin biological polymers like proteins and DNA into their characteristic shapes.

Hydrogen bonds are classified as weak bonds because they are easily and rapidly formed and broken under normal biological conditions.

non-polar In addition to polar covalent bonds, there are nonpolar covalent bonds. An electron density plot for the H 2 molecule shows that the shared electrons occupy a volume equally distributed over BOTH H atoms. Electron Density for the H 2 molecule

Nonpolar covalent bonds In biological systems, if a molecules has a predominance of nonpolar covalent bonds, that substance is hydrophobic. (very important)

The hydrophobic effect is another unique property of water caused by the hydrogen bonds. The hydrophobic effect is particularly important in the formation of cell membranes.

Hydrophilic properties (between polar molecules) Hydrophilic properties are very important because they allow molecules to be soluble in water. (because most living organisms are mostly water this is a good thing)

amphipathic molecules Molecules with a polar/ionized region at one end and a non-polar region at the other end hydrophilic hydrophobic

If amphipathic molecules are mixed with water, the molecules form clusters with the polar (hydrophilic) regions at the surface, where they will come into contact with water, and the non-polar (hydrophobic) regions nestled in the center of the cluster away from contact with water. The arrangement will increase the overall solubility in water.

Hydrophilic: Hydrophobic: Example: mix salad oil with water shake to break H bonds but as these bonds reform between water molecules, they push the oil molecules out of the way-the oil tends to cluster together in drops or as a layer on the water s surface-thereby exposing less surface area to the water

Bond strength In biological systems, covalent bonds are called strong bonds. This means that they are not normally broken under biological conditions unless by enzymatic catalysis. This is in opposition to weak bonds such as ionic bonds which are easily broken under normal biological conditions of temperature and pressure.

Van der Waals interactions probably the most basic type of interaction. Any two molecules experience Van der Waals interactions.

due to the spatial orientation of the molecules, the attractive forces outweigh the repulsive ones.

Even macroscopic surfaces experience VDW interactions VDW forces are electrostatic in nature

strongest covalent ionic hydrogen Van der Waals weakest