Chemistry 1120 Unit 5: Chapter 11.1-11.3 & 20: Organic Chemistry

Amines

An amine group is simply a nitrogen atom that has three single bonds to H atoms or *R Groups*. Amines can be thought of as derivatives of ammonia, with one H atom replaced by R (a primary amine), two H atoms replaced by R (a secondary amine), or three H atoms replaced by R (a tertiary amine)

Ethers

An ether has a general formula R-O-R', where R sf R' may or may not be different hydrocarbon groups. Th oxygen atom is sp3 hybridized. The difference in electronegativities of oxygen and carbon means that ethers are slightly polar. However, this slight dipole is not enough to make simple alkyl ethers soluble in water. The C-O-C linkage is important in chemistry because it can function as a connector between molecules.

Three-Dimensional Formula

In order to represent different molecular shapes in three dimensions, chemists use a three-dimensional formaula, which is similar to the structural formula except that some bonds as drawn as wedges.

Alkyl Amines

In simple, alkyl amines, the N atom is sp3 hybridized, giving *tetrahedral geometries*. Due to the electronegativity of nitrogen, amines are polar molecules with a partial negative charge on the N atom.

Chair Conformation

In this configuration, all C-C-C bond angles in the ring are 111.4 degrees, so there is minimal angle strain. In addition, the chair conformation has staggered C-H and C-C bonds all around the ring.

R,S System

In this system, each group of the chirality centre is assigned according to the Cahn-Ingold-Prelog Rules. Priorities are assigned as the numbers 1,2,3, and 4 with 1 being the highest priority group and 4 the lowest. The molecule is "viewed" from the opposite side as the lowest priority group. If the sequence is counterclockwise, then the configuration is S. If arranged in clockwise from 1 to 3 then configuration is R.

Plane Polarized Light

Light in which electric field waves oscillate in only one plane.

Organic Molecules

Molecules containing carbon combined with several other elements such as hydrogen, nitrogen, oxygen and sulfur.

Enantiomers

Molecules that are nonsuperimposable mirror images of each other. The molecule cannot be superimposed onto its mirror image. If we swing the mirror image around to try to superimpose the two, we find that there is no way to get all four substituent atoms to align together. This type of isomerism is known as chirality

Benzene Ring

Recall that the lewis structure of benzene rings have alternating single and double bonds, which gives two resonance forms.What is really happening here is that the six p orbitals (one from each carbon atom) are overlapping to form pi molecular orbitals over the entire ring. Each C-C bond is actually equivalent, and the bond lengths are identical between the bond lengths for single and double bonds.

Index of Hydrogen Deficiency (IHD)

The number of missing hydrogen atoms divided by two. Every double bond means that there are two fewer hydrogen atoms than the parent formula. Every triple bond means that there are 4 fewer hydrogen atoms (IHD=2). And every cyclic structure means that there are two fewer hydrogen atoms (IDH=1 per ring). The IDH is therefore the count of the number of pi bonds and rings (units of unsaturation) that are present within a structure.

Acyl Functional Groups

The difference between the various acyl functional group and an aldehyde or ketone is that a substituent that is not hydrogen or an alkyl group is bonded to the central carbon. Rather, the substituent is a polar group that is often displaced during reactions.

What causes fragrances and odours?

When we inhale certain molecules called odourants, they bind with olfactory receptors in our noses. This interaction sends a nerve signal to our brain that we experience as a smell. Most common smells are caused by organic molecules.

Cis-Trans Isomerism in Alkenes

cis and trans isomers are diastereomers because they are nonsuperimposable, but are not mirror images of each other. Diastereomers have different physical and chemical properties. The cis-trans labels work well for disubstituted alkenes and are commonly used. However, for alkenes in which there are three or four different substituents, these labels become ambiguous.

Halides

A Halide is the simplest functional group. It is simply a halogen atom, usually denoted as X, where X is F, Cl, Br, or I. Halogen molecules are more electronegative than carbon, which means that *C-X bonds are polar*. *The carbon bonded to a halogen atom has a partial positive charge*. All organic halides are polar molecules except in cases where individual bond dipoles cancel out, as in a molecule like tetrachloromethane. The bond dipole between carbon and a halogen atom in turn affect the bond polarity of adjacent bonds.

Aromatic Hydrocarbons

A class of organic compounds that are closely related to conjugated alkenes. The more important type of aromatic structure is the benzene ring. Aromatic hydrocarbons are often referred to as *arenes*. When an arene unit is a substituent on another group, it is called an *aryl group*.

Family

A group of organic compounds with the same functional group forms a family. For example, alcohols are a family of compounds that have an -OH group.

Stereoisomerism

A type of isomerism in which the connectivity between atoms is identical, but the spatial arrangements of atoms are different. Stereoisomerism can be conformational or configurational. *Conformational Isomerism* is the result of bond rotations. Conformational isomers can be interconverted simply by rotating around single bonds, without breaking any bonds. *Configurational isomers* can only be interconverted by breaking bonds.

Alcohols

Alcohols are organic compounds containing the -OH group, or hydroxyl group, and they have the general formula R-OH. The oxygen atom is sp3 hybridized, giving C-O-H bond angles that are close to the ideal tetrahedral bond angle of 109.5 degrees. The slightly smaller bond angle is due to the effect of lone pair repulsions. Oxygen atoms are very electronegative, whereas carbon atoms are not. The difference in electronegativity leads to a very polar C-O bond. The O-H bond is also very polar, which leads to a strong hydrogen bonding between alcohol molecules. Hydrogen bonding can also occur in water molecules, which makes many alcohols soluble in water, even with the presence of nonpolar hydrocarbon components. However, as the size of the nonpolar hydrocarbon component increases, aqueous solubility decreases.

Chirality Centre

Any carbon atom with four different substituents in a tetrahedral arrangement. The molecules on the left and right are nonsuperimposable mirror images and are enantiomers of one another.

Carbonyls- Aldehydes and Ketones

Both aldehydes and ketones contain a carbonyl group. Ketones have an R group attached to both sides of the carboxyl group, while aldehydes have one R group and a hydrogen atom. ( An exception is methanal, which is an aldehyde, with two H atoms attached to the carboxyl group). Carbonyls have an important resonance structure in which the carbon atom has a formal positive charge.

Structural Isomers

Butane and isobutane are structural isomers, molecules with the same molecular formula but different structures. Because of their different structures, they ave different properties: they are indeed different compounds. Isomerism is ubiquitous in organic chemistry. Butane has two structural isomers. Pentane (C5H12) has 3, Hexane (C6H14) has 5 and Decane (C10H22) has 75!

Equatorial and Axial Bonds

C-H bonds that are arranged around the plane of the ring pointing outward are described as equatorial bonds and those pointed vertically up and down, perpendicular to the ring, are called axial bonds.

Carbon's ability to form double and triple bonds

Carbon atoms also form double bonds (trigonal planar geometry) and triple bonds (linear geometry), adding even more diversity to the number of compounds that carbon forms. In contrast, silicon (the element in the periodic table with properties closest to that of carbon) does not readily form double or triple bonds because the greater size of silicon atoms results in a Si-Si bond that is too long for much overlap between non hybridized p orbitals.

Carbon's tendency to Catenate

Carbon, more than any other element, can bond to itself to form chain, branched, and ring structures. Although other elements can form chains, none beat carbon at this ability. Silicon, for example, can form chains with itself. However silicons affinity for oxygen (the Si-O bond is stronger than Si-Si bond) coupled with the prevalence of oxygen in the atmosphere means that Si-Si chains are readily oxidized to form silicates (the silicon oxygen compounds that compose a significant portion of minerals). By contrast, the C-C bond and the C-O bond are nearly the dame strength, allowing carbon chains to exist relatively peacefully in an oxygen rich environment. Silicons affinity for oxygen robs it of the rich diversity that catenation provides carbon.

Carbon's Tendency to form four covalent bonds

Carbon, with its four valence electrons, forms four covalent bonds. The geometry about a carbon atom forming four single bonds is tetrahedral (as shown in methane). Carbon's ability to form four bonds, and to form those bonds with a number of different elements, results in the potential to form many different compounds. Always remember to draw carbon with four bonds.

Chemical Behaviour in a Chiral Environment

Chiral compounds also exhibit different chemical behaviour when they are in a chiral environment (a chiral environment is simply one that is not superimposable on its mirror image)

Chirality

Chirality is important, not only to organic chemistry, but also biochemistry and biology. Most biological molecules are chiral and usually only one of the other enantiomer is active in biological systems. Some of the enantiomers are indistinguishable from one another and differ from one another in two important ways: 1.) The direction in which they rotate plane-polarized light and 2.) In their chemical behaviour in a chiral environment.

Conformational Isomerism: Rotation About Single Bonds

From bonding in alkanes we know that rotation about a single bond is to be expected because of axial symmetry of sigma bonds. The various molecular shapes that result from the rotation about single bond are known as *conformers* (from conformational isomers) or *rotamers* (from rotational isomers).

Alkenes

Have double bonds between carbon atoms. The simplest alkene is ethene, C2H4. The carbon atoms involved in a double bond are sp2 hybridized. The two sp2 orbitals on each carbon form sigma bonds with a hydrogen or another atom, and one sp2 orbital from each carbon atom overlap to form a sigma bond, which is a part of the double bond. The p orbitals on each carbon atom overlap to form a pi bond. Rotation around C=C double bonds requires significant energy in the form of heat or light. The reason is that pi bond locks the molecule in place around the two carbons of the double bond., with approximate angles of 120 degrees to fit the sp2 hybridization. Rotation around a double bond is possible if the alkene is strongly heated or if the molecule absorbs a photon of appropriate energy.

Alkanes

Have only single bonds between carbon atoms. The simples alkane is methane, CH4. We saw that the carbon atom in methane is sp3 hybridized and the four C-H bonds are sigma bonds, arranged in a tetrahedron. In higher alkanes with two or more carbon atoms, each carbon atom is sp3 hybridized and the C-C and C-H bonds are all sigma bonds with tetrahedral geometry. Sigma bonds are symmetrical around the imaginary axis connecting the two atoms. This symmetry gives largely unrestricted rotation about the C-C single bonds in an alkane. Alkanes are "flexible" molecules because rotation can occur around each C-C bond. The rotation is not entirely free though.

Alkynes

Have triple bonds between carbon atoms. The C-C triple bond in alkynes is made up of one sigma bond and two pi bonds. Alkynes have linear geometry due to sp hybridization of the carbon atoms. The C-C bond has a very high bond energy.

Polycyclic Aromatic Hydrocarbons (PAHs)

Have two or more benzene rings that are connected. As in benzene, each carbon atom is sp2 hybridized and pi molecular orbitals are shared over the entire molecule. The structure of some common polycyclic aromatic hydrocarbons contain fused rings.

Hydrocarbons

Hydrocarbons are compounds that contain only carbon and hydrogen. They are the simplest type of organic compounds and are commonly used as fuels. Candle wax, oil, gasoline, and natural gas are all composed of hydrocarbons. Hydrocarbons provide the structural backbone for all organic compounds, which makes them good starting materials in the synthesis of many different products such as dyes, pharmaceuticals, plastics, and rubber.

Types of Hydrocarbons

Hydrocarbons can be classified as open chain hydrocarbons or cyclic hydrocarbons. Cyclic hydrocarbons involve carbon atoms that are arranged to form one or more ring structures. ex. cyclohexane. Hydrocarbons are also classified according to the type of bonds between carbon atoms.

Unsaturated Hydrocarbons

Hydrocarbons that have fewer hydrogen atoms than the maximum for that number of carbon atoms. *Unsaturation occurs whenever rings or pi bonds are present in the structure*.

Saturated Hydrocarbons

Hydrocarbons with the maximum number of hydrogen atoms for the number of carbons present.

Conjugated Alkenes

In Alkenes with two or more C-C double bonds, the relative location of the double bonds can affect the properties of the molecule.

Newton Projection

In a Newton Projection formula, we look directly down the C-C bond of interest.

Amines next to a Benzene Ring

In amines that are next to a benzene ring, the lone pair on the nitrogen atom can become part of the delocalized pi bonding. This would suggest that the nitrogen atom should be sp2 hybridized. As it turn out, the structure of aniline suggests that the hybridization of nitrogen is somewhere between sp2 and sp3. Aniline is not planar, it is a bent structure.

Conjugation

In conjugation, the p orbitals overlap to give delocalized pi bonding across all the sp2 hybridized carbons that are linked. This occurs whenever a molecule has a sequence of three or more sp2 hybridized atoms. Conjugation leads to a planar molecular structure.

Constitutional Isomers

Molecules with the same molecular formula but different structures. Because of their different structures, they have different properties, they are indeed different compounds. The more carbon atoms you have in a molecular formula, the more constitutional isomers are possible. The number and variety of constitutional isomers for a given molecular formula become more complicated when rings, double, or triple bonds can be present. Another variation of constitutional isomerism involving functional groups is when the same functional group can be located in different positions in different molecules.

Functional Groups

Most other families of organic compounds can be thought of as hydrocarbons with one or more functional groups: a characteristic atom or group of atoms, inserted into the hydrocarbon. The insertion of a functional group into a hydrocarbon alters the properties of the compound significantly. For example, methanol; which can be thought of as methane with a functional group -OH substituted for one of the hydrogen atoms, is a polar, hydrogen bonded liquid at room temperature. Methane, in contrast, is a nonpolar gas. The -OH groups gives methanol a completely different set of physical and chemical properties from its parent hydrocarbon methane.

Stereoisomerism II: Configurational Isomerism

Occurs when atoms and functional groups are connected in same sequence, but there is a difference in the spatial locations of atoms or groups. The only way to in convert configurational isomers is to break covalent bonds. They can be divided into two categories: *Enantiomers* are molecules that are nonsuperimposable mirror images. *Diasteromers* are molecules that are nonsuperimposable but are not mirror images.

Heteroatoms

Organic compounds that contain atoms other than carbon and hydrogen. The presence of heteroatoms changes how the parent formula is determined: 1. Each Halogen atom is considered to be equivalent to a hydrogen atom. 2. Oxygen atoms do not change the number of hydrogen atoms in the parent formula. 3. Each nitrogen atom requires one additional hydrogen atom in the parent formula.

Amides

Part of the Acyl Functional group family. Amines are very unreactive in comparison to other members of this family. The stability comes from the resonance structures. Another way of looking at this is that the p orbital on the N atom becomes part of a delocalized pi system over the O-C-N bonds. As a result the amide group is *planar*. The relative unreavtivity of amides comes from the partial double bond between carbon and nitrogen, which is difficult to break. This is very important biologically because proteins are made of amino acids that are connected together by amide groups, which are called peptide bonds in biochemistry,

E,Z System

The IUPAC system for naming substituent alkenes and is based on assigning priorities to each pair of substituent bonded to each carbon of the double bond. A configuration of *Z* is assigned if the high priority groups are on there same side of the bond; a configuration of *E* is assigned if the high priority groups are on different sides.

Absolute Configuration

The actual configurations of atoms at a chirality centre. Once the absolute configuration is known, it is labelled according to the *R,S System*

Halogen Atomic Sizes

The atomic sizes of halogens increase down the group (F<Cl<Br<I). Similarly, C-X bond lengths also vary, with C-F bonds being shortest and C-I bonds being longest.

Carbon Skeleton Formula

The carbon skeleton formula (also called line formula) shows the carbon-carbon bonds only as lines. Each end or bend of a line represents a carbon atom bonded to as many hydrogen atoms as necessary to form a total of four bonds. Carbon skeleton formulas allow you to draw complex structures quickly.

Condensed Structural Formula

The condensed structural formula groups the hydrogen atoms with the carbon atom to which they are bonded. Condensed structural formulas may show some of the bonds or none at all. The condensed structural formula for butane can also be written as CH3CH2CH2CH3.

Induction Effect

The partial positive charge on carbon 1 pulls electron density from the second carbon atom, which polarizes the C-C bond. This is known as an inductive effect and can occur in bonds that are adjacent to a polar functional group.

Why carbon is so unique

The reasons for carbon' s uniqueness and versatile behaviour include its ability to form four covalent bonds, its ability to form double and triple bonds, and its ability to catenate (to form chains).

The Carboxylic Acid Family

The structure and bonding of a carboxylic acid group is very similar to that of carbonyls, accept the additional -OH group modifies the chemical behaviour. Several other functional groups can be viewed as being derived from carboxylic acids. All of these groups share what is called an *acyl group*, RCO.

Structural Formula

The structure of a particular hydrocarbon is represented with a structural formula, a formula that shows not only the numbers of each kind of atoms, but also how the atoms are bonded together. Organic chemists use several different kinds of structural formulas. The structural formula shows all of the carbon and hydrogen atoms in the molecular and how they are bonded together. Note: that structural formulas are generally not 3-D representations of the molecule: as space filling or ball and stick models are, but rather 2-D representations that show how atoms are bonded together. As such, the most important feature of a structural formula is the *connectivity* of the atoms, not the exact way the formula is drawn. We represent double and triple bonds in structural formulas with double or triple lines. The kind of structural formula we use depends on how much information we want to portray.

Organic Chemistry

The study of compounds containing carbon combined with one or more elements such as hydrogen, nitrogen, oxygen and sulfur, including their properties and their reactions. Organic chemistry is also to basis for living organisms. Life has evolved based on carbon containing compounds, making organic chemistry of utmost importance to any person interested in understanding living organisms.

Cahn-Ingold-Prelog Rules

Used to determine the priorities of substituents. *Rule 1:* Priority is first determined on the basis of th atomic mass of that atoms that are directly bonded to the carbons in the double bond. *Rule 2:* If the atoms directly attached to a double bonded carbon atom are the same, then the second atoms of the substituents are compared. Again, priority is assigned on the basis of atomic mass. If there is no difference in the priority of the second atoms, then the third atoms are considered, and so on. *Rule 3*: If the substituent contains a double or triple bond, the multiply bonded atom is treated as if it were two or three atoms bonded to the same carbon.