base pairing in dna

Base Pairing in DNABase Pairing in DNA

Red = ORed = OGrey = CGrey = C

White = HWhite = HPurple = KPurple = K

Ionic RadiiIonic RadiiLiLi++ = 0.68 Å = 0.68 ÅNaNa++ = 0.97 Å = 0.97 ÅKK++ = 1.33 Å = 1.33 Å

RbRb++ = 1.47 Å = 1.47 Å

Cavity Size (O-O Dist.) Cavity Size (O-O Dist.) = 1.40 Å= 1.40 Å

KK++ fits best fits best

Crown Ether, CCrown Ether, C1212HH2424OO66 (18-Crown-6) (18-Crown-6)

Rules for Predicting Molecular Rules for Predicting Molecular GeometryGeometry

 1.  Sketch the Lewis structure of the molecule or 1.  Sketch the Lewis structure of the molecule or ionion

2.  Count the electron pairs and arrange them in 2.  Count the electron pairs and arrange them in the way that  minimizes electron-pair repulsion.the way that  minimizes electron-pair repulsion.

3.  Determine the position of the atoms from the 3.  Determine the position of the atoms from the way the electron pairs are shared.way the electron pairs are shared.

4.  Determine the name of the molecular structure 4.  Determine the name of the molecular structure from the position of the atoms.from the position of the atoms.

5.  Double or triple bonds are counted as one 5.  Double or triple bonds are counted as one bonding pair when predicting geometry.bonding pair when predicting geometry.

 Note: The same rules apply for molecules that contain more than one central atom

The DipoleThe Dipole    A dipole arises when two electrical charges of equal A dipole arises when two electrical charges of equal

magnitude but opposite sign are separated by distance.magnitude but opposite sign are separated by distance.

The dipole moment The dipole moment (())

= Qr 

where Q is the magnitude of the charges and r is the distance

The sum of these vectors will give us the dipole for the The sum of these vectors will give us the dipole for the moleculemolecule

For a polyatomic molecule we treat the dipoles as 3D vectors

Overlap of OrbitalsOverlap of Orbitals

The point at which the potential energy is a minimum

is called the equilibrium bond distance

The degree of overlap is determined by the system’s potential energy

equilibrium bond distance

2s

These new orbitals are called hybrid orbitals

The process is called hybridization

What this means is that both the s and one p orbital are involved in bonding to the connecting

atoms

Formation of sp hybrid orbitalsFormation of sp hybrid orbitals

The combination of an s orbital and a p orbital produces 2 new orbitals called sp orbitals.

Formation of spFormation of sp22 hybrid orbitalshybrid orbitals

Formation of spFormation of sp33 hybrid orbitalshybrid orbitals

Hybrid orbitals can be used to explain bonding Hybrid orbitals can be used to explain bonding and molecular geometryand molecular geometry

Multiple BondsMultiple Bonds 

Everything we have talked about so far has only dealt with what we call sigma bonds

 Sigma bondSigma bond () A bond where the line of electron A bond where the line of electron density is concentrated symmetrically along the line density is concentrated symmetrically along the line connecting the two atoms.connecting the two atoms.

Pi bondPi bond () A bond where the overlapping regions A bond where the overlapping regions exist above and below the internuclear axis (with a exist above and below the internuclear axis (with a nodal plane along the internuclear axis).nodal plane along the internuclear axis).

Example: HExample: H22C=CHC=CH22

Example: HExample: H22C=CHC=CH22

Example: Example: HCHCCHCH

Delocalized Delocalized bonds bonds When a molecule has two or more resonance structures,

the pi electrons can be delocalized over all the atoms that have pi bond overlap.

In general delocalized bonding is present in all molecules where we can draw resonance structures with

the multiple bonds located in different places.

Benzene is an excellent example.  For benzene the orbitals all overlap leading to a very delocalized electron

system

Example: CExample: C66HH66 benzene benzene

The one that is lower in energy is called the bonding orbital,

The one higher in energy is called an antibonding orbital.

These two new orbitals have different energies. 

BONDING

ANTBONDING

Moleculuar Orbital (MO) TheoryMoleculuar Orbital (MO) Theory

Energy level diagrams / molecular Energy level diagrams / molecular orbital diagramsorbital diagrams

MO Theory for 2nd row diatomic MO Theory for 2nd row diatomic moleculesmolecules

 Molecular Orbitals (MO’s) from Atomic Orbitals (AO’s) 1. 1. # of Molecular Orbitals = # of Atomic Orbitals# of Molecular Orbitals = # of Atomic Orbitals

2.2. The number of electrons occupying the Molecular orbitals is equal The number of electrons occupying the Molecular orbitals is equal to the sum of the valence electrons on the constituent atoms.to the sum of the valence electrons on the constituent atoms.

3.3. When filling MO’s the Pauli Exclusion Principle Applies (2 electrons When filling MO’s the Pauli Exclusion Principle Applies (2 electrons per Molecular Orbital)per Molecular Orbital)

4. 4. For degenerate MO’s, Hund's rule applies.For degenerate MO’s, Hund's rule applies.

5.5. AO’s of similar energy combine more readily than ones of different AO’s of similar energy combine more readily than ones of different energyenergy

6.6. The more overlap between AOs the lower the energy of the The more overlap between AOs the lower the energy of the bonding orbital they create and the higher the energy of the bonding orbital they create and the higher the energy of the antibonding orbital.antibonding orbital.

Example: Example: LiLi22

MOs from 2p atomic orbitalsMOs from 2p atomic orbitals

1) 1 sigma bond through overlap of orbitals along the internuclear axis.

2) 2 pi bonds through overlap of orbitals above and below (or to the sides) of the internuclear axis.

Interactions between the 2s and 2p Interactions between the 2s and 2p orbitalsorbitals

The 2s and 2p molecular

orbitals interact with each other so as to lower the energy of the 2s MO and

raise the energy of the 2p MO.

For B2, C2, and N2 the interaction is so strong that the 2p is pushed higher in energy than 2p orbitals

Paramagnetism of OParamagnetism of O22