Molecular Representations Organic Chemistry Second Edition David Klein Chapter 2 Molecular Representations

Representing Molecules There are many ways to represent molecules Drawing Lewis structures are most time consuming

Representing Molecules There are 3 constitutional isomers of propanol Constitutional Isomers: compounds with same molecular formula but different connectivity between atoms. 

Representing Molecules

Representing Molecules There are 3 constitutional isomers of propanol

Representing Molecules Much time to draw Lewis structure of large molecules Antibiotic Amoxicillin (below). Lewis structure is cluttered, and time consuming to draw

Bond-line Structures The Bond-line structure is easier to read and to draw

Bond-line Structures Looks odd because C atoms are not labeled Clearer way for (bio)chemists to communicate

Bond-line Structures Lines between atoms are covalent bonds (Like Lewis str) Atoms and bonds are drawn along a zigzag that represent the geometry of the bond angles Here, the C are sp3 hybridized: bond angle is 109.5

Bond-line Structures Lines between atoms are covalent bonds Carbon atoms are not labeled. Carbon (C) is imagined at each endpoint, vertex, and valley 2 4 6 1 3 5

Bond-line Structures The H of C-H bonds are NOT drawn We know the number of H atoms on a C because we know the valence of C is 4 C1 is attached to 1 carbon; 3 H that are “hidden” C2 is attached to 2 carbons; 2 H that are “hidden” C3 is attached to 2 carbons; 2 H that are “hidden” 2 4 6 1 3 5

Bond-line Structures Interpret the number and location of H atoms in a molecule H atoms are not shown, but there are enough to complete the octet (4 bonds) to carbon

Bond-line Structures How many number C- and H-atoms in each structure below

Bond-line Structures Double bonds and triple bonds are drawn to show their sp2 and sp3 geometries, respectively spx spx spx spx

Bond-line Structures What is atom geometry of a sp2 center? sp center? spx spx spx spx

Bond-line Structures Correct linear geometry

Bond-line Structures Practice bond-line structures: This is how I will draw molecules from now on. Number of C Number of H

Bond-line Structures Be able to convert Lewis structure or condensed structure to bond-line structure Represent the bond angles with zigzags Follow VSEPR and spread out the electron pairs on a central atom Why is this “bad”?

Bond-line Structures Single bonds can rotate around axes REPEAT: Single bonds can rotate

Bond-line Structures Single bonds can rotate around axes REPEAT: Single bonds can rotate Redraw the top structure after a bond rotation

Bond-line Structures Heteroatoms (atoms other than C and H) ARE LABELED with all hydrogen atoms. Lone pairs e– are optional UNLESS instructed to show them NEVER draw a carbon with more than 4 bonds!!

Bond-line Structures Practice: Draw bond-line representations for the following Lewis structures

Bond-line Structures Draw a bond-line structures for the molecule: CH2CH(CH2)4CH3 CH2CH(CH2)4CH3 Subscript 4 means 4 CH2 units in a row CH2CH(CH2)4CH3 These Cs are connected CH2CH(CH2)4CH3 This C is connected to 1 C and 2 H (that’s 3 bonds); What is the 4th bond?

Indentifying Functional Groups Draw bond-line structures for the chemical reaction This C is connected to 2 CH3 groups, 1 H, and another C. If difficult to visualize, then draw Lewis structure

Indentifying Functional Groups Draw bond-line structures for the chemical reaction This C is connected to 2 CH3 groups and another C. What is the 4th bond type?

Indentifying Functional Groups Certain atoms bonded in specific arrangements, undergo specific chemical reactions These atom arrangements are called functional groups Functional groups are the reaction centers!

Indentifying Functional Groups More functional groups are listed in table alcOHol KEYtone something on “Ether” side of O KEYtone with ‘de Hydrogen’ Re: meTHIONine “Thion” = sulfur Thion+alcohol = thiol “Carbon/oxy” + OH acid Writing the mnemonic as an answer on an exam results in NO credit

Indentifying Functional Groups

Bond-line Structures with Formal Charge Identify formal charges (fc) in bond-line representations fc’s hints where reactive centers are Label all formal charges (lone pair e– are shown)

Bond-line Structures with Formal Charge Neutral carbon atoms in a molecule have 4 covalent bonds Sometimes carbon will have a +1 charge. How many bonds will carbon have? Why are these CARBOCATIONS unstable?

Bond-line Structures with Formal Charge Sometimes carbon will have a -1 charge. What makes CARBANIONS unstable? If carbon carries a charge in a molecule, the charge MUST be shown on the bond-line structure

Bond-line Structures and Lone Pair Electrons Optionally lone pairs are omitted from bond-line strs. lone pair e– can be determined, if neutral OR (+) or (-) form. chrg. is added

Bond-line Structures and Lone Pair Electrons Optionally lone pairs are omitted from bond-line strs. lone pair e– can be determined, if neutral OR (+) or (-) form. chrg. is added If the formal charge is indicated, you can determine how many lone pairs e– are present

Bond-line Structures and Lone Pair Electrons To calculate the number of lone pair e– for an atom Note the formal charge Compare the number of valence electrons that should be associated with the atom to the number of valence electrons that are actually associated with an atom (including 1 e– from each covalent bond) Add appropriate number of e– to obtain the formal charge

Bond-line Structures and Lone Pair Electrons However: You can’t determine the formal charge on an atom unless you know how many e– there are on the atom You must ALWAYS draw formal charges on a bond-line structure to eliminate confusion

Bond-line Structures and Lone Pair Electrons How many lone pairs are on the oxygen atom below?

Bond-line Structures and Lone Pair Electrons Neutral O should have 6 valence e– (group 6: periodic table) It has a -1 charge (above), so it has one additional e– (6+1=7) assigned 1 e– is from O–C covalent bond HOW many lone pairs does O have above?

3D Bond-line Structures We will use dashed and solid wedges to show groups that point back into the paper or out of the paper to represent a 3D molecule on a 2D piece of paper

Resonance Remember from General Chemistry, what is resonance? Does the allyl carbocation have resonance contributors?

Resonance Drawing lines between atoms inadequately represents covalent bonds in molecules with resonance Determine hybridization of the carbons in the allyl carbocation Calculate the steric number for each carbon (# of σ bonds + # lone pairs) When the steric number is 3, each C is sp2 hybridized

Resonance If all of the carbons have unhybridized p orbitals, they can overlap All three overlapping p orbitals allow the electrons to move throughout the overlapping area simultaneously That’s RESONANCE!!

Resonance The π e–exist on both sides of the molecule, so two resonance contributors represent the structure Brackets indicate that both resonance contributors exist simultaneously

Resonance Because neither of the contributors exists, the average (or hybrid) is much more appropriate vs. δ+ δ+ two contributors resonance hybrid Analogy: a nectarine is a hybrid formed by mixing a peach and a plum. A nectarine is NOT sometimes a peach and sometimes a plum. It is always a “hybrid” i.e., a nectarine.

Resonance Resonance makes a molecule MORE stable Delocalization of electrons Electrons can span a greater distance electrons have more freedom to minimize repulsions Electrons spend time close to multiple nuclei all at once maximizing attractions Delocalization of charge The charge is spread out over more than one atom. The resulting partial charges are more stable than a full +1 charge. δ+ δ+ resonance hybrid

Curved Arrows in Resonance We have used curved arrows to show electron movement Curved arrows generally show electron movement for pairs of electrons The arrow starts where the electrons are currently located The arrow ends where the electrons will end up after the electron movement

Curved Arrows in Resonance Rules for using curved arrows to show RESONANCE bond electrons and lone pair e– can be mobile. Never break a single bond when drawing RESONANCE structures Resonance occurs for electrons existing in overlapping p orbitals and adjacent lone pair e– while electrons in single bonds (σ bonds) are NOT involved in RESONANCE.

Curved Arrows in Resonance Rules for using curved arrows to show RESONANCE Never exceed an octet for 2nd row elements (B, C, N, O, F) I.e., never move electrons toward and sp3 atom How about this arrow?

Curved Arrows in Resonance Rules for using curved arrows to show RESONANCE 2nd row elements (B, C, N, O, F) will rarely but sometimes have LESS than an octet i.e. if 2 atoms are sp2 and attached via a pi-bond, the electrons in π bond can move toward either atom and leave a formal charge behind However, the π e- will typically favor the more electronegative atom What will the resonance hybrid look like for this structure?

Formal Charge in Resonance When using curved arrows to show RESONANCE, often structures will carry a formal charge that must be shown Draw the resonance contributor indicated by the arrows below Are any of the rules violated? Show any formal charges on the contributors

Formal Charge in Resonance In the resonance, the arrows tell us how to move the electrons to create the other contributor NOTE: Lone pairs can be moved toward sp2 atom Draw arrows showing the resonance in the reverse direction You can also think of the arrows as showing the direction that charge will flow

Patterns in Resonance There are 5 main bonding patterns in which resonance occurs. Recognize these patterns to predict when resonance will occur Allylic lone pairs Allylic positive charge Lone pair of electrons adjacent to a positive charge (sp2 atom) π bond between two atoms with different electronegativities Conjugated π bonds in a ring There are examples in the next few slides

Patterns in Resonance Vinyl atom: directly bonded to C=C double bond Allyl atom: one atom away from a C=C double bond “atom–single bond=double bond” (ALLYLIC WORDS) Label the vinylic chlorides and the allylic chlorides

Patterns in Resonance Identifying allylic lone pairs Circle all of the allylic lone pairs Draw arrows on each structure to show resonance

Patterns in Resonance Identifying allylic lone pairs For each, show the resulting resonance contributor and all formal charges Practice with conceptual check point 5

Patterns in Resonance Dealing with allylic positive charge Only one curved arrow is needed If there are multiple double bonds (conjugated), then multiple contributors are possible. Show the resonance contributors and curved arrows below Draw a resonance hybrid Practice with conceptual checkpoint 6

Patterns in Resonance A lone pair adjacent to a positive charge Only one arrow is needed Explain how the formal charges are affected by the electron movement in the following examples

Patterns in Resonance A lone pair adjacent to a positive charge Consider the resonance in the NITRO group ALLYLIC WORDS: “atom–single bond=double bond” Draw all possible resonance contributors

Patterns in Resonance A π bond between atoms of different electronegativity The π electrons will be more attracted to the more electronegative atom Why are formal charges are created by the electron movement?

Patterns in Resonance Conjugated pi bonds in a ring Each atom in the ring MUST have an unhybridized p orbital that can overlap with its neighbors Electrons can be shown to move clockwise or counterclockwise What type of motion do the electrons actually have? Practice with conceptual checkpoint 1

Patterns in Resonance Summary figure

Patterns in Resonance Show all of the resonance contributors for the following molecule Notice that carbons with 4 bonds (sp3) isolate areas of resonance from one another

1 Stability of Contributors How do we assess the stability of resonance contributors? Formal charge generally DECREASES stability, especially a +1 charge on an electronegative atom or -1 on a low electronegativity atom COMPLETE OCTETS INCREASE stability Draw the three resonance contributors for acetic acid Assess the stability of each contributor, and draw a resonance hybrid

1 Stability of Contributors Draw a reasonable resonance contributor for the following molecule

1 Stability of Contributors The octet rule is usually a bigger factor than formal charge when assessing stability For each structure, assess the stability of each contributor, and draw a resonance hybrid

2 Delocalized vs. Localized Generally, lone pairs adjacent to a C=C double bond are capable of resonance, but not in this case. The electron movement above does not violate any of our rules, so why can’t the Nitrogen’s lone pairs be delocalized? - see next slide

2 Delocalized vs. Localized Recall that delocalized electrons must exist in an unhybridized p orbital overlapping with p orbitals on neighboring atoms The Nitrogen’s lone pair is positioned perpendicular to the plane where the other pi electrons reside Practice with SkillBuilder

Additional Practice Problems How many carbon and hydrogen atoms are in the following molecule?

Additional Practice Problems Draw the bond-line structures from the following formulas: C(CH3)3CN Cl2CH(CH2)5CO2H CH3CHBrCH(NH2)C(CH3)3

Additional Practice Problems Fill in any necessary formal charge on the molecule below

Additional Practice Problems Fill in any necessary lone pairs in the structure below

Additional Practice Problems Show the curve arrows that leads to the resonance contributor where the topmost O loses its charge and the carbocation also loses its charge