What are the forces in a molecular structure
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Torsional strain: Strain between groups on adjacent atoms. A-B-C-D. Worst when eclipsed; best when staggered . Bond angle strain: when a bond angle, A-B-C, diverges from the ideal (180, 120, 109). What are the forces in a molecular structure?. 120 deg. View from here yields view below.

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What are the forces in a molecular structure?

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What are the forces in a molecular structure

Torsional strain: Strain between groups on adjacent atoms.

A-B-C-D. Worst when eclipsed; best when staggered.

Bond angle strain: when a bond angle, A-B-C, diverges from the ideal (180, 120, 109)

What are the forces in a molecular structure?


Rotation about c2 c3 in butane

120 deg.

View from here yields view below.

View from here yields view below.

Rotation about C2 – C3 in butane

Gauche conformation, Methyls closer, 60 deg, more repulsion, higher energy

Anti conformation Methyls 180 deg, lower energy

Anti!!

Gauche!!


Energy profile for rotation in butane

Energy Profile for Rotation in Butane

Three hills (eclipsed) 120 apart.

Three valleys (staggered forms) 120 apart;


Problem rotational profile of 2 methylbutane about c2 c3

Problem: Rotational profile of 2-methylbutane about C2-C3.

First, staggered structures.

300

60

180

Rotate the front Me group.

Relative energies….


Now eclipsed

Now, eclipsed….

180

240

120

360 = 0

0

This was the high energy staggered structure,180 deg. Shown for reference only.

Now relative energies…..


Now put on diagram

Now put on diagram…

eclipsed

staggered

120

60

360

300

180

240

0


Conformations of cycloalkanes cyclopropane

Conformations of cycloalkanes: cyclopropane

Planar ring (three points define a plane); sp3 hybrization: 109o.

Hydrogens eclipsing. Torsional angle strain.

Bond angle strain. Should be 109 but angle is 60o.

Cyclopropane exhibits unusual reactivity for an alkane.


Conformation of cyclobutane

Folded, bent: less torsional strain but increased bond angle strain

Conformation of cyclobutane

Fold on diagonal

Planar: eclipsing, torsional strain and bond angles of 90o


Cyclobutane molecular dynamics

Cyclobutane molecular dynamics


Cyclopentane

Cyclopentane


Cyclohexane

Boat conformation

Chair conformation

Cyclohexane

Ideal solution: Everything staggered and all angles tetrahedral.


Chair conformation

Axial:

Equatorial:

Chair Conformation


Axial and equatorial

Axial and Equatorial

Axial Up/Equatorial Down: (A/E)

Equatorial Up/Axial Down: (E/A)

A/E

E/A

E/A

A/E

A/E

E/A


Ring flips

Ring Flips

Chair

Boat or

Twisted Boat

A becomes E

E becomes A

Up stays Up

Down stays Down

Chair


Substituents axial vs equatorial

Substituents: Axial vs Equatorial


Substituent interactions

Each repulsion is still about 3.6 kJ. Note that the gauche interaction in butane is about 3.8.

Substituent Interactions

Destabilizes axial substituent. Each repulsion is about 7.28/2 kJ = 3.6 kJ

1,3 diaxial repulsions

Alternative description:

gauche interactions


Newman projection of methylcyclohexane

Newman Projection of methylcyclohexane

Axial methyl group

Equatorial methyl group

gauche

anti


Disubstituted cyclohexanes

7.3 kJ (axial)

7.3 kJ (axial)

Disubstituted cyclohexanes

1,2 dimethylcyclohexane

3.6 kJ (gauche)

3.6 kJ (gauche)

interactions

0.0 kJ equatorial

0.0 kJ equatorial

7.3 + 3.6 = 10.9 kJ

7.3 + 3.6 = 10.9 kJ


What are the forces in a molecular structure

7.3 kJ (axial)

0.0 kJ equatorial

3.6 kJ (gauche)

0.0 kJ equatorial

7.3 kJ (axial)

0.0 kJ + 3.6 kJ = 3.6 kJ

14.6 kJ + 0.0 kJ = 14.6 kJ

diequatorial

diaxial


When does the gauche interaction occur

When does the gauche interaction occur?


Translate ring planar structure into 3d

Translate ring planar structure into 3D

E/A

A/E

A/E

Assume the tert-butyl group is equatorial.

E/A

A/E

E/A

Energy accounting

No axial substituents

One 1,2 gauche interaction between methyl groups, 3.6 kJ/mol

Total: 3.6 kJ


Problem which has a higher heat of combustion per mole a or b

Problem: Which has a higher heat of combustion per mole, A or B?

7.3

3.6

3.6

3.6

7.3

18.2

7.2

More repulsion, higher heat of combustion by 11.0 kJ/mol


Trans and cis decalin

Trans and Cis Decalin

Now build cis decalin, both same side.

Build trans decalin starting from cyclohexane, one linkage up, one down

Trans sites used on the left ring

Cis sites used on left ring.

Trans sites used on the right ring

Cis sites used on right ring.

Trans decalin

Locked, no ring flipping

Cis decalin, can ring flip


Trans fusions determine geometry

Trans fusions determine geometry

What is the geometry of the OH and CH3?

E/A

A/E

A/E

E/A

E/A

A/E

Trans fusions, rings must use equatorial position for fusion. Rings are locked.

The H’s must both be axial

Work out axial / equatorial for the OH and CH3.

OH is equatorial and CH3 is axial


Stereoisomerism and chirality

Stereoisomerism and Chirality


Isomerism

Isomerism

Constitutional Isomers: Same atoms but linked (bonded) together differently. Spatial orientation not important.

No, different molecular formulae!!

Are these constitutional isomers of hexane?

Are these constitutional isomers of cis but-2-ene?

Not this one! It is 2-butene. Cis / trans does not matter.


Stereoisomerism

Stereoisomerism

Stereoisomers: Same molecular formulae, same connectivity; same constitutional isomer. Different spatial orientation of the bonds.

Are these stereoisomers of cis but-2-ene?

How does the connectivity differ between these two?


Enantiomers and diastereomers

Enantiomers and Diastereomers

Two kinds of Stereoisomers

Enantiomers: stereoisomers which are mirror objects of each other. Enantiomers are different objects, not superimposable.

Diastereomers: stereoisomers which are not mirror objects of each other.

If a molecule has one or more tetrahedral carbons having four different substituents then enantiomers will occur. If there are two or more such carbons then diastereomers may also occur.


What are the forces in a molecular structure

Summary of Isomerism Concepts

Isomers, contain same atoms, same formula

Constitutional isomers, different connectivities, bonding.

Stereoisomers, same connectivity, different three dimensional orientation of bonds

Enantiomers, mirror objects

Diastereomers, not mirror objects


Mirror objects carbon with 4 different substituents we expect enantiomers mirror objects

Mirror Objects – Carbon with 4 different substituents. We expect enantiomers (mirror objects).

Reflect!

The mirror plane still relates the two structures. Notice that we can characterize or name the molecules by putting the blue in the back, drawing a circle from purple, to red, to green. Clockwise on the right and counterclockwise on the left. Arbitrarily call them R and S.

Notice how the reflection is done, straight through the mirror!

Arrange both structures with the light blue atoms towards the rear….

These are mirror objects. Are they the same thing just viewed differently ?? Can we superimpose them?

We can superimpose two atoms. but not all four atoms.

R

S


Recap tetrahedral carbon with four different substituents enantiomers

Recap: Tetrahedral Carbon with four Different Substituents. Enantiomers

Mirror objects. Different, not superimposable.

Enantiomers

Simple Rotation, Same

Simple Rotation, Same


But the reflection might have been done differently position the mirror differently

But the reflection might have been done differently. Position the mirror differently….

Reflection can give

any of the following…

Again. all three objects on the right are the mirror object of the structure above. They are different views of theenantiomer.

A swap of two substituents is seen to be equivalent to a reflection at the carbon atom.

Can you locate the mirror which would transform the original molecule into each mirror object?

What is common to each of these reflection operations?

In the course of each reflection, two substitutents are swapped. The other two remain unchanged.

All three of these structures are the same, just made by different mirrors. The structures are superimposable. What rotations of the whole molecules are needed to superimpose the structures?


Now superimposable mirror objects tetrahedral carbon with at least two identical substituents

Now Superimposable mirror objects: Tetrahedral Carbon with at least two identical substituents.

Reflection can interchange the two red substituents. Clearly interchanging the two reds leads to the same structure, superimposable! Remember it does not make any difference where the mirror is held for the reflection.

This molecule does not have an enantiomer; the mirror object is superimposable on the original, the same object.


Summary

Summary

A reflection on a tetrahedral carbon with four different substituents produces a different, non-superimposable structure, the enantiomer. A different three dimensional arrangement of the bonds is produced, a differentconfiguration.

Such a carbon is called chiral. The carbon is a chiral center, a stereogenic center.

If a tetrahedral carbon has two or more substituents which are the same then reflection produces the same structure, the same configuration. Such a carbon is called achiral.

The swapping two of the substituents on the chiral carbon is equivalent to a reflection.

There is only one mirror object produced by reflection, no matter where the mirror is located. It is either the same as the original structure (superimposable) or it is different (non-superimposable), the enantiomer.


Multiple reflections

Multiple reflections

One reflection (swap of substituents) on a chiral carbon produce the enantiomer.

Two reflections (swaps) yields the original back again.

Even number (0, 2, 4…) of reflections (swaps) on a chiral carbon yields the original structure. An odd number (1, 3, 5…) yields the enantiomer.

Enantiomers

Enantiomers

One swap

Second swap

Same molecule.


Repeating

Repeating….

Three different substitutents.

Reflection (in this plane) yields.

Same, not enantiomers.

Four different substituents.

Reflection (in this plane) yields.

Different, not superimposble, enantiomers.


Is a chiral carbon needed no

Is a chiral carbon needed? No!

Recall allene:

Reflection (in this plane) yields.

Different, not superimposable, enantiomers.

The (distorted) tetrahedral array of the substitutents (huh??) suffices to allow for enantiomers.


Naming of configurations

Naming of configurations.

S

R

A priority is assigned to each substituent on the chiral carbon

Rotate the structure so that the lowest priority towards the rear.

Draw an arc from the highest, to the next lower, to the next lower.

If arc is clockwise it is R configuration. If arc is counterclockwise it is S.


Assigning priorities 2

Assigning Priorities 2

Start with first atom attached to chiral carbon

C vs. F


When the first atom is the same examine what is bonded to it

When the first atom is the same…Examine what is bonded to it.

Start with first atom attached to chiral carbon. No decision!!

Examine atoms bonded to first atom

O vs O

N vs C


Example assigning priorities

Example: assigning Priorities

S configuration

Substituents

Highest,1

Lowest, 4

3

2

Assign on the basis of the atomic number of the first atom in the substituent.

If the atoms being compared are the same examine the sets bonded to the atoms being compared.

C has priority over H!!


What are the forces in a molecular structure

More… If the first atom is the same and the second shell is the same then proceed to the atoms attached to the highest priority of the second shell.

Examine the first atom, directly attached to the chiral atom.

Examine the atoms bonded to the first atom (the second shell) .

N vs N

C vs C

H vs H

Examine atoms bonded to highest priority of second shell, N

Cl vs F Cl wins!


Unsaturation

Unsaturation

So far have not worried about double or triple bonds.

Double and triple bonds are expanded as shown below.

Expanded into

becomes


Let s investigate what happens if low priority is positioned closer to us than chiral carbon

Let’s investigate what happens if low priority is positioned closer to us than chiral carbon…

H towards the rear where it belongs…

Now let’s swap any two substituents. We know that this produces the enantiomer, R. Swap the H and the Cl.

Arc going in wrong direction because the low priority substituent is closer to us than the chiral center!!!!!!

We are looking at the molecule from the wrong side.

INVERT NAMING if LOW PRIORITY IS CLOSER THAN CHIRAL CENTER:

Clockwise is S

Counterclockwise is R


Physical properties of enantiomers

Physical Properties of Enantiomers

Enantiomers: different compounds but have same

Melting Point

Boiling Point

Density

Enantiomers rotate plane polarized light in opposite directions.

OPTICALLY ACTIVE!!

The enantiomers rotate plane polarized light the same amount but in opposite directions. One clockwise; the other counterclockwise.


How to know if a compound is optically in active symmetry elements

How to know if a compound is optically (in)active. Symmetry elements.

The symmetry of an object is described in terms of symmetry elements. The use of a symmetry element may only interchange identical atoms.

Proper Rotation. Rotation about an axis. Think of a propeller.

Reflection plane (mirror plane).

Inversion Point. An equidistant line through the center of the molecule.

Improper Rotation. Rotation followed by reflection in plane perpendicular to axis.

If a molecule has a reflection plane, inversion point, or improper rotation axis: inactive

The presence of any of these symmetry elements except for proper rotation rules out enantiomers.


Rotational axis

Rotational Axis


Reflection plane

Reflection Plane


Inversion point

Inversion Point


Improper rotational axis

Improper Rotational Axis


What are the forces in a molecular structure

Allene, let’s find the symmetry elements in it.

Two Proper Rotational Axes, 180 deg.

Reflection Plane

Reflection Plane

We recognize this molecule as being achiral because of the reflection planes or because of the improper rotational axis. Usually they go together. Can you, however, design a molecule having an improper axis but not reflection planes.

Proper Rotational Axis, 180 deg

Improper Rotational Axis, 90 and 270 deg


Polarimeter

Polarimeter

before

after

Concentration: pure liquid in g/mL; solution in g per 100 mL of solvent


Optical activity

Optical Activity

Optically Active compounds rotate plane polarized light. Chiral compounds (compounds not superimposable on their mirror objects) are expected to be optically active.

Optically Inactive compounds do not rotate plane polarized light. Achiral compounds are optically inactive.


Problems

Problems…

If the specific rotation of pure R 2-bromobutane is 48 degrees what is the specific rotation of the pure S enantiomer?

The pure S enantiomer has a specific rotation of -48 degrees.

Equal but opposite!!


Mixtures of enantiomers

Mixtures of Enantiomers

These are high school mixture problems.

If you know the specific rotation of the pure enantiomers and the composition of a mixture then the specific rotation of the mixture may be predicted. And conversely the specific rotation of the mixture may be used to calculate the composition of the mixture.

Specific rotation of mixture = (fraction which is R)(specific rotation of R)

+ (fraction which is S)(specific rotation of S)


Example

Example

Mixture of 30% R and 70% S enantiomer.

The pure R enantiomer has a specific rotation of -40 degrees.

What is the specific rotation of the mixture?

Contribution from R

Contribution from S


What are the forces in a molecular structure

Using the specific rotation to obtain the composition of the mixture.

For the same two enantiomers ([a] of R = -40) , suppose the specific rotation of a mixture is 8. degrees what is the composition?

Specific rotation of mixture = (fraction which is R)( specific rotation of R)

+ (fraction which is S)( specific rotation of S)

-40.

8.

+ (1. – fraction which is R)

40.

Fraction which is R = 40%; fraction which is S is 60%.


Racemic mixtures racemates

Racemic Mixtures, Racemates

The racemic mixture (racemate) is a 50:50 mixture of the two enantiomers.

The specific rotation is zero.

The racemic mixture may have different physical properties (m.p., b.p., etc.) than the enantiomers.


Optical purity enantiomeric excess

Optical Purity, Enantiomeric Excess

Consider a mixture which is 80% R (and 20% S). Assume the specific rotation of the pure R enantiomer is 50 degrees.

As before

Specific rotation of mix = 0.80 x 50. + .20 x (-50.)

= 30.

R R R R R

R R R S S

Now, recall that a racemic mixture is 50% R and 50% S. Mixture is 60% R and 40% racemic.

Specific rotation of mix = 0.60 x 50. + .40 x (0.)

= 30.

The optical purity (or enantiomeric excess) is 60%.


Fischer projection

Fischer Projection

Cl to Ethyl to Methyl

Reposition to

Look from this point of view.

Standard Fischer projection orientation:

vertical bonds recede

horizontal bonds come forward

H,low priority substituent, is closer so CCW is R.

R and S designations may be assigned in Fischer Projection diagrams. Frequently there is an H horizontal making R CCW and S CW.

Standard short notation:


Manipulating fischer projections

Manipulating Fischer Projections

Even number of swaps yields same structure; odd number yields enantiomer.

1 swap

or

R

or

Etc.

S

All of these represent the same structure, the enantiomer (different views)!!


Manipulating fischer projections1

Manipulating Fischer Projections

Even number of swaps yields same structure; odd number yields enantiomer.

2 swaps

or

R

or

Etc.

R

All of these represent the same structure, the original (different views)!!


Rotation of entire fischer diagrams

Rotation of Entire Fischer Diagrams

Rotate diagram by 180 deg

Same Structure simply rotated: H & Br still forward; CH3 &C2H5 in back.

This simple rotation is an example of “proper rotation”.

Rotation by 90 (or 270) degrees.

Enantiomers. Non superimposable structures! Not only has rotation taken place but reflection as well (back to front). For example, the H is now towards the rear and ethyl is brought forward.

This combination of a simple rotation and reflection is called an “improper rotation”.


Multiple chiral centers

Multiple Chiral Centers

S

Do a single swap on each chiral center to get the enantiomeric molecule.

R

S

R

Each S configuration has changed to R.

Now do a single swap on only one chiral center to get a diastereomeric molecule (stereoisomers but not mirror objects).

R

S

S

R


Multiple chiral centers1

Multiple Chiral Centers

Enantiomers

Enantiomers

S

R

S

R

R

S

S

R


Multiple chiral centers2

Multiple Chiral Centers

S

R

Diastereomers

S

R

R

S

Diastereomers

S

R


Diastereomers

Diastereomers

Everyday example: shaking hands. Right and Left hands are “mirror objects”

R --- R is enantiomer of L --- L

and have equivalent “fit” to each other.

R --- L and L --- R are enantiomeric, have equivalent “fit”, but “fit” differently than R --- R or L – L.


Diastereomers1

Diastereomers

Require the presence of two or more chiral centers.

Have different physical and chemical properties.

May be separated by physical and chemical techniques.


Meso compounds

Meso Compounds

Must have same set of substituents on corresponding chiral carbons.

S

R

R

S

As we had before here are the four structures produced by systematically varying the configuration at each chiral carbon.

S

R

S

R


Meso compounds1

Meso Compounds

What are the stereochemical relationships?

S

R

Enantiomers

Mirror images, not superimposable.

R

S

Diastereomers.

S

R

S

R

Mirror images! But superimposable via a 180 degree rotation. Same compound.

Meso


Meso compounds characteristics

Meso Compounds: Characteristics

Has at least two chiral carbons. Corresponding carbons are of opposite configuration.

Can be superimposed on mirror object, optically inactive.

Can demonstrate mirror plane of symmetry

Molecule is achiral. Optically inactive. Specific rotation is zero.

R

S

S

R

Meso

Can be superimposed by 180 deg rotation.


Meso compounds recognizing

Meso Compounds: Recognizing

What of this structure? It has chiral carbons. Is it optically active? Is it meso instead?

Assign configurations.

Looks meso. But no mirror plane.

R

S

Rearrange by doing even number of swaps on upper carbon.

Now have mirror plane.

R

Original structure was meso compound. In checking to see if meso you must attempt to establish the plane of symmetry.

S

Meso


Cycloalkanes

Cycloalkanes

Vertical reflection plane.

Horizontal reflection plane.

Look for reflection planes!

There are other reflection planes as well. Do you see them?

Based on these planar ring diagrams we observe reflection plane and expect optical inactivity….

But the actual molecule is not planar!! Examine cyclohexane.

This plane of symmetry (and two similar ones) are still present. Achiral. Optically inactive. The planar diagrams predicted correctly.


Substituted cyclohexanes

Substituted cyclohexanes

The planar diagram predicts achiral and optically inactive. But again we know the structure is not planar.

cis

Mirror objects!!

This is a chiral structure and would be expected to be optically active!!

But recall the chair interconversion….

Earlier we showed that the two structures have the same energy. Rapid interconversion. 50:50 mixture. Racemic mixture. Optically Inactive. Planar structure predicted correctly


What are the forces in a molecular structure

More…

trans

No mirror planes. Predicted to be chiral, optically active.

Enantiomer.

Ring Flips??????

R,R

R,R

trans 1,2 dimethylcyclohexane

Each structure is chiral. Not mirror images! Not the same! Present in different amounts. Optically active!

Other isomers for you… 1,3 cis and trans, 1,4 cis and trans.


Resolution of mixture into separate enantiomers

Resolution of mixture into separate enantiomers.

Mixtures of enantiomers are difficult to separate because the enantiomers have the same boiling point, etc. The technique is to convert the pair of enantiomers into a pair of diastereomers and to utilize the different physical characteristics of diastereomers.

Formation of diastereomeric salts. Racemic mixture of anions allowed to form salts with pure cation enantiomer.

Racemic mixture reacted with chiral enzyme. One enantiomer is selectively reacted.

Racemic mixture is put through column packed with chiral material. One enantiomer passes through more quickly.


Chirality in the biological world

Chirality in the Biological World

A schematic diagram of an enzyme surface capable of binding with (R)-glyceraldehyde but not with (S)-glyceraldehyde.

All three

substituents

match up

with sites

on the

enzyme.

If two are matched up then the third will fai!


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