Organic Chemistry 101: Bonding

A molecular orbital formed by combining two or more atomic orbitals from different subshells.

Hybrid orbitals are named for the atomic orbitals and subshells (s, p, or d) from which they are formed. For example, ​sp hybridization includes one s orbital and one p orbital, while sp3 hybridization includes one s orbital and three p orbitals.

A bond formed between two orbitals that directly overlap head-to-head. Sigma bonds are the strongest type of covalent bond.

All covalent bonds contain exactly one sigma bond, though they may have one or two pi bonds as well.

A bond formed between two orbitals oriented parallel to one another, overlapping side-to-side. In other words, two lobes of one molecular orbital overlap with two lobes of another molecular orbital.

In order for a pi bond to form, a sigma bond must also be present.

A single bond has no pi bonds; it contains only a single sigma bond.

A double bond has one pi bond and one sigma bond.

In order for a pi bond to form, a sigma bond must first be present.

A triple bond has two pi bonds and one sigma bond.

In order for a pi bond to form, a sigma bond must first be present.

It is displayed when one s orbital hybridizes with three p orbitals, forming four equivalent sp3 orbitals.

A carbon atom with sp3 hybridization forms single bonds to four different atoms. A classic example of this bond arrangement is methane. For other central atoms, note that lone pairs also contribute to overall hybridization.

An sp3-hybridized carbon atom has tetrahedral geometry.

When an atom is surrounded by four single bonds, they will exist in the most symmetric arrangement possible, a tetrahedron with bond angles of 109.5º.

It is displayed when an s orbital hybridizes with two p orbitals, forming three equivalent sp2 orbitals.

A carbon atom undergoing sp2 hybridization will form bonds to three total atoms, with a mix of two single bonds and one double bond. A classic example of this bond arrangement is methanal. For other central atoms, note that lone pairs also contribute to overall hybridization.

trigonal planar

When an atom is surrounded by three bonds (and no lone pairs), they will exist in the most symmetric arrangement possible, a planar triangle with bond angles of 120º.

It is displayed when an s orbital hybridizes with one p orbital, forming two equivalent sp orbitals.

A carbon atom undergoing sp hybridization will form bonds to two atoms. These can include either two double bonds or a single and triple bond. A classic example of this bond arrangement is carbon dioxide.

linear

When an atom is surrounded by two bonds (and no lone pairs), they will exist in the most symmetric arrangement possible, a straight line with bond angles of 180º.

tetrahedral

Since the central carbon is bonded to four atoms, it is sp3 hybridized. This means that the four atoms are arranged around it in a tetrahedron.

trigonal planar

Since the central carbon is bonded to three atoms, it is sp2 hybridized. This means that the three atoms are arranged in a planar triangle.

tetrahedron

Since each carbon atom is bound to four other atoms (one bromine, two hydrogens, and one carbon), they are both sp3 hybridized. Hence, the atoms around each are arranged tetrahedrally.

planar triangle

Since each carbon atom contains three bonds (two single bonds to the hydrogens and a double bond to the other carbon, or two single bonds to the chlorines and a double bond to the other carbon), they are both sp2 hybridized. Hence, the atoms around each one is arranged in a planar triangle.

straight line

Since the carbon atom in question contains two bonds (one single bond to the carbon and one triple bond to the nitrogen), it is sp hybridized. Hence, the atoms around it are arranged in a straight line. The other terminal carbon is sp3 hybridized.

The most common depiction of a carbon backbone involves the carbon atoms in a zig-zag line, with hydrogens branching off of each carbon.

This is a visual representation of the most stable state of a set of sp3 hybridized carbons.

C5H12 or pentane

This picture is a structural formula, which is a two-dimensional graphical depiction of the molecule’s shape.

hexane

This is an example of formula nomenclature, in which the geometric information in the structural formula is assumed. It is commonly given without the hyphens between carbons, which would be CH3(CH2)4CH3 in this case.

C4H10 or butane

A skeletal formula of an organic molecule, instead of this full structural form. In such a depiction, the hydrogens can be assumed, and each vertex of the chain represents a carbon atom.

Structurally, no significant difference exists. Both molecules are resonance forms of the same molecule (in this case, analine).

The two structures will look indistinguishable from each other. They can be represented by the 3D structure above.

Resonance increases stability.

Resonance is one of the most common ways that an organic molecule can be stabilized. Having several resonance forms is a strong indication that the molecule can be synthesized easily.

It occurs when a molecular system, typically a carbon chain, contains an alternating system of pi and sigma electrons.

Conjugation drastically increases stability. For example, benzene is fully conjugated and is extremely stable.

It undergoes resonance because the alternating pi-sigma-pi system allows the weakly bound pi electrons to shift one position along the chain.

The structures above show how the electrons in aniline, a benzene ring with an attached amine group, move from one position to the next. This shifts the pi-sigma-pi system.

Heteroatoms, or non-carbon atoms in a carbon chain, can be included in the system.

For example, propenal contains a terminal double (pi) bond to oxygen, then a single (sigma) bond between carbons, then another double bond. This alternating system represents conjugation even though it includes oxygen, a non-carbon atom. Another common heteroatom is nitrogen.

Lone pairs and carbocations can be included in the system.

For example, cyclopropene has a single, double, single, cation arrangement. The cation can move to the adjacent carbon, and the double bond can then shift over one position as well. This creates three resonance structures.

Yes, this 1,3,butadiene system is conjugated.

It contains the alternating pi-sigma-pi bond system that is characteristic of conjugation.

The resonance structures shown above add to overall stability, though each is significantly less stable than 1,3-butadiene's original structure.

Yes, the non-bonded electrons on the negatively charged carbon are available to participate in a pi system, as shown below.

In this case, the heteroatom oxygen resonates to accept the negative charge.

No. Since the double bonds are adjacent (at carbons 2 and 3) without an intervening single bond, the overall molecule cannot be conjugated.

Triple bonds are the strongest, then double bonds, while single bonds are the weakest.

This occurs because a triple bond includes both a sigma bond and two additional pi bonds, while a double bond includes both a sigma bond and one additional pi bond.

Single bonds are the longest, then double bonds, while triple bonds are the shortest.

Simply imagine that the bonds are pulling the atoms together. The stronger the bond, the harder it pulls, and the shorter the gap between atoms becomes.

A single bond is fairly rigid in the direction of the bond itself; it can stretch and vibrate only slightly in this direction.

On the other hand, a single bond is quite flexible in the direction of rotation around the bond itself. Singly bonded structures (such as conformational isomers) are free to rotate to assume their most stable configuration.

A double bond is fairly rigid in all dimensions. It can stretch and vibrate only slightly in any direction.

Specifically, double-bonded structures are not free to rotate to assume their most stable configurations, and as a result can be locked in a less-stable configuration (such as cis/trans isomers).

An additional form of a molecule. Isomers always have the same molecular formula, but differ in some fundamental fashion.

While many types of isomers exist, two main categories are constitutional isomers (which differ in their bonding) and stereoisomers (which differ in their atoms' spatial arrangement).

Also known as a structural isomer, it differs from the original molecule in the way its atoms are bonded to one another.

While constitutional isomers share a molecular formula, they are fundamentally different molecules and thus can have different chemical and physical properties. Of all the classifications of isomers, constitutional isomers are the least similar.

It differs from the original molecule only in its rotation around a single bond.

Molecules can freely interchange from one conformational isomer to another, and will preferentially assume the most stable conformation. Of all of the classifications of isomers, conformational isomers are the most similar.

A two-dimensional projection of a molecule, shown as if the molecule was being viewed directly along a C-C bond.

In this Newman projection of ethane, the central point with three black H's represents the carbon close to the viewer, while the larger circle with three red H's represents the carbon behind it.

It effectively shows the arrangement of the functional groups around the carbon atoms, showing whether they overlap one another or are staggered apart.

Specifically, they allow the relative stability of various conformers to be determined easily. The more staggered the functional groups, the more stable the conformer will be.

1. staggered

2. eclipsed

These conformations are not specific to ethane; they can exist around any C-C single bond (in propane, butane, etc).

staggered

Staggered arrangements are more stable because they "spread out" the functional groups. In the eclipsed conformation, on the other hand, a larger amount of electrostatic repulsion exists between the closely overlapping groups. This repulsion is known as torsional strain.

1. anti conformation

2. gauche conformation

These forms are determined by the location of the two largest groups bound to each carbon. In the anti configuration, these groups are 180º apart; in the gauche configuration, they are only 60º apart. The example above shows anti and gauche butane.

anti conformation

Since it minimizes torsional strain, the maximum possible separation of the large groups will be the most stable conformation. The anti configuration places these groups the farthest apart, and is thus more stable.

An organic molecule is an isomer in which the bonding between atoms is equivalent, but the spatial arrangement of the bonds differs.

Like all isomers, stereoisomers have identical formulas but are not identical compounds.

A form of stereoisomer in which two molecules differ in their physical shapes.

Geometric isomers come in two primary forms: when functional groups differ in their location around a double bond and when they differ in their location on a ring. Geometric isomers usually involve positioning around a double bond.

Geometric isomers have different physical properties, such as boiling point, melting point, and solubility. For this reason, they can be separated using standard techniques such as distillation or recrystallization.

1. cis-2-butene

2. trans-2-butene

Their structures are shown below:

Cis and trans nomenclature only applies if one hydrogen is present on each side of the double bond. The cis form contains the large groups on the same side of the bond, while the trans form has the large groups positioned across from one another.

1. E-1-chloro-2-butene

2. Z-1-chloro-2-butene

E and Z nomenclature applies if at least one side of the double bond does not contain a hydrogen atom. In the Z isomer, the largest groups are on the same side of the bond (remember "ze zame zide"). In the E isomer, the largest groups on the opposite side (remember the "epposite side").

Z-2-bromo-2-butenal

In E/Z nomenclature, the functional group with the higher atomic number takes priority. In this case, the 2-carbon is bound to two groups: an aldehyde and bromine; Br has a higher atomic number than carbon, giving it a higher priority. Since it is positioned on the same side of the double bond as the methyl group, this is the Z isomer.

Molecules can rotate plane-polarized light if they are chiral.

Chiral compounds are those with non-superimposable mirror images.

The opposite of "chiral" is "achiral."

To identify a chiral carbon as R or S, follow this procedure:

1. Number all 4 substituents from 1 to 4, with the highest atomic number substituent as #1, the next highest as #2, and so on.

2. Draw an arrow from 1 to 2 to 3. This arrow will point either clockwise or counterclockwise.

3. If the arrow points clockwise AND the 4th-priority group is pointing backwards, the carbon is the R form. If it points counterclockwise, the carbon is S.

4. If the 4th-priority group points forwards, switch the configuration that would have been obtained from step #3.

This chiral center has an R configuration.

Br, with the highest atomic number, is prioritized #1. O, the next highest, is #2, while C is #3. H has the lowest atomic number, giving it a priority of #4. The first-, second-, and third-priority substituents are arranged in a clockwise direction (R). Since this hydrogen is already pointing backwards, no rearrangement is necessary.

This chiral center has an R configuration.

O, with the highest atomic number, is given #1 priority. The propyl group is the next highest, giving it #2 (since it contains bonds to carbons instead of the hydrogens present on methyl, which is given #3). Finally, H is #4. However, since OH is pointing towards the back, the hydrogen must currently be facing forwards; in other words, we are viewing the back of this molecule. This means that when a line is drawn from 1 to 2 to 3 (in the counterclockwise, or S, direction), the actual configuration would be R (clockwise) if that large substituent were flipped to the front.

Also known as a stereocenter, is a carbon that contains single bonds to four different substituents.

In this image, notice that the mirror molecule of a chiral carbon cannot be superimposed over the original.

A type of stereoisomer that is the non-superimposable mirror image of an original molecule.

Molecules can only have enantiomers if they contain at least one chiral carbon. Note that enantiomers must differ in their configuration at each and every stereocenter.

Yes

Since this carbon is bound to four unique substituents, it cannot be superimposed on its mirror image, making it chiral.

No

A chiral carbon must be bound to four unique substituents. As such, any carbon that makes a double bond cannot possibly be chiral.

No

This carbon does have 4 single bonds (including one to a hydrogen that is not shown), and a carbon in a ring structure certainly can be chiral. In this particular case, however, the ring is identical on both sides of the carbon in question, making it achiral.

A stereoisomer that is not the mirror image of an original molecule.

Several forms of diastereomers exist, but the most common includes molecules that differ at some, but not all, of their chiral carbons. Molecules that do differ at all of their stereocenters are enantiomers.

Since diastereomers differ in their physical shape, they can have different physical properties. For this reason, they can be separated using standard techniques such as distillation and recrystallization.

Examples of properties which can be used in this way are melting point, boiling point, and solubility.

A 50/50 mixture of a pair of enantiomers. Note that racemic mixtures are achiral overall.

Most chiral chemicals exist in racemic mixtures; the primary exceptions are biologically active compounds, since most enzymes are stereoselective. Since enantiomers cannot be separated directly, racemic mixtures are notoriously difficult to separate.

Enantiomers can be differentiated by the direction that they rotate plane-polarized light (PPL).

This relates to the fact that isolated enantiomers are optically active compounds. One enantiomer will rotate PPL a given amount in a clockwise direction, while the other will rotate it by the same amount, but in the opposite direction.

A racemic mixture cannot be separated using standard lab practices. To resolve two enantiomers, the following procedure must be followed:

1. React the mixture with an optically active compound, creating a mix of two diastereomers.

2. Separate the diastereomers using their differing physical properties.

3. Chemically break apart the diasteromers, recreating the enantiomers that were present in the original racemic mixture.

A two-dimensional "flattening" of a three-dimensional molecule.

The substituents in the horizontal axis point out of the plane of the page, while those along the vertical axis point into the page.

A molecule that contains both chiral centers and an internal plane of symmetry. Though its carbons are chiral, the overall molecule is achiral.

The chiral centers on one side of the line of symmetry will rotate light in one direction, while those on the other side will rotate it the opposite way. So, a meso molecule does not rotate plane polarized light.

enantiomers

These molecules differ at their only chiral center; the molecule on the left is S while the molecule on the right is R. As enantiomers, they are non-superimposable mirror images of each other.

diastereomers

The molecules share one chiral carbon with the same configuration (S, circled at the top), and one chiral carbon with opposite configurations (one is R, one is S, circled at the bottom). Thus, they are non-superimposable and are not mirror images.

They are the same compound and meso.

In both depictions, this molecule has an internal plane of symmetry, making it achiral. The two compounds are the same, since the mirror image of the compound on the left is superimposable over the compound on the right.