Molecular Structure

Molecular Structure Both atoms and molecules are quantum systems We need a method of describing molecules in a quantum mechanical way so that we can predict structure and properties The method we use is the Linear Combination of Atomic Orbitals where we can use the properties of atoms to predict the properties of molecules.

Molecular Structure We combine atoms to form molecules by considering the phase of the atomic orbitals we are using We represent the phase via the shading we give the orbital. The phase represents the sign of the wavefunction

Molecular Structure We combine atoms to form molecules by considering the phase of the atomic orbitals we are using The phase represents the sign of the wavefunction We represent the phase via the shading we give the orbital.

Molecular Structure For an s orbital, the orbital has the same phase everywhere: For a p orbital, there is a change in the sign of the wavefunction across the nodal plane: 1s orbital, n = 1, l = 0 2p orbital, n = 2, l = 1, ml = -1

Molecular Structure • Consider two H atoms (1s1) coming together from infinite separation. • There are two possibilities: • The wavefunctions are in phase • The wavefunctions are not in phase

Molecular Structure • Case 1: The wavefunctions are in phase • The atoms move together and the electron waves overlap with the same phase, producing constructive interference and a build up of electron density between the nuclei • The energy of the system drops and we form a bond

r = 8 Å r = 3 Å r = 7 Å r = 2 Å r = 6 Å r = 1 Å r = 5 Å r = 0.75 Å

Molecular Structure • Case 2: The wavefunctions are out of phase • The atoms move together and the electron waves have opposite phase. • The electron waves overlap producing destructive interference and electron density between the nuclei is reduced. • The energy of the system rises and we have an antibonding situation

r = 8 Å r = 3 Å r = 2 Å r = 7 Å r = 5 Å r = 1 Å r = 4 Å r = 0.75 Å

Two atoms with wavefunctions in phase overlap with constructive interference. Electron density increases between the nuclei and the overall energy decreases. • When the wavefunctions are of opposite phase, the electron density between the nuclei decreases due to destructive interference. The energy of the system rises and we have an antibonding situation Bonding Antibonding

Bonding Antibonding

Organic Structure and Bonding Review of diatomic bonding There are two types of bond that are important in this part of the Periodic Table s bonds and p bonds

Organic Structure and Bonding s bonds and p bonds s bonds are in general stronger than p bonds and can be formed from either s or p orbitals:

Organic Structure and Bonding s bonds and p bonds s bonds have no nodal plane that contains the two nuclei. The s* antibonding orbital has a nodal plane between the two nuclei

Organic Structure and Bonding s bonds and p bonds p bonds have a nodal plane that contains both nuclei, The p* antibonding orbital also has a plane between the nuclei

Organic Structure and Bonding s bonds and p bonds These s, p bonding orbitals and s*, p* antibonding orbitals are the orbitals that are used to bind all simple organic molecules together. We can also describe the bonding in diatomic molecules important models for larger organic systems

Organic Structure and Bonding s bonds and p bonds To describe the bonding in the diatomic molecules such as O2, N2 and X2 (X = F, Cl, Br and I), we use both the s orbitals and the p orbitals on the two atoms as a basis set - the palette of atomic orbitals from which we will build the molecular orbitals. The energies of the two different l states, s and p, are slightly different in polyelectronic atoms.

Organic Structure and Bonding s bonds and p bonds The s orbitals and the p orbitals appear as follows

Organic Structure and Bonding s bonds and p bonds We arrange the atoms along one of the axes for convenience and so the first pair of orbitals we construct are the ss and ss* orbitals from the s orbitals on the atoms.

Organic Structure and Bonding s bonds and p bonds We now us the higher energy p orbitals to construct ps and pp orbitals

Organic Structure and Bonding s bonds and p bonds The complete molecular orbital diagram for all the diatomic molecules from Li2 to N2

Organic Structure and Bonding s bonds and p bonds The complete molecular orbital diagram for all the diatomic molecules from Li2 to N2 As each molecule has a different number of electrons, Li2 2 Be2 4 B2 6 C2 8 N2 10 O2 12 F2 14 Ne2 16

Organic Structure and Bonding s bonds and p bonds Li2 2 Be2 4 B2 6 C2 8 N2 10 O2 12 F2 14 Ne2 16 We can write the electronic structure of each molecule by placing electron pairs into the orbitals.

Organic Structure and Bonding s bonds and p bonds Li2 2 Be2 4 B2 6 C2 8 N2 10 O2 12 F2 14 Ne2 16 Something peculiar happens after N2 Recall that as the charge on the nucleus increases, the orbitals become more stabilized and the electrons become more strongly bound.

Organic Structure and Bonding s bonds and p bonds Li2 2 Be2 4 B2 6 C2 8 N2 10 O2 12 F2 14 Ne2 16 This happens by different amounts, depending on the orbital. After N2 (10 e-), the ordering of the orbitals derived from p change their order in the molecule

Organic Structure and Bonding s bonds and p bonds For N2 (10 e-), the ordering is this For O2 (12 e-), the ordering is this

Organic Structure and Bonding s bonds and p bonds This is an example of configurational interaction Each electron moves in the field of the other electrons. If the energies of the two molecular orbitals are sufficiently close and the nodal properties are correct, molecular orbitals will interact and shuffle their energies in the molecule. This causes the s orbitals to change their energetic ordering but only when the nuclear charge is high enough to force the electrons close in energy.

Organic Structure and Bonding s bonds and p bonds Configurational interaction Each electron moves in the field of the other electrons. If the energies of the two molecular orbitals are sufficiently close and the nodal properties are correct, molecular orbitals will interact and shuffle their energies in the molecule. This causes the s orbitals to change their energetic ordering but only when the nuclear charge is high enough to force the electrons close in energy.

Molecular Structure A full description of the structure of a molecule requires the solution of the Schrödinger equation for the entire molecule. The potential term is far too complicated to be solved analytically and so we need an empirical approach to molecular structure.

Molecular Structure There are two common approaches - Lewis description - Valence Shell Electron Pair Repulsion (VSEPR) theory and both are based on the electron count at the central atom of the molecule or fragment of the molecule.

Molecular Structure Lewis description The covalent chemical bond can be thought of as a pair of electrons shared between atoms; By considering the number of electrons in the valence shell and the number of electrons in the outer atoms, we can explain the presence of lone pairs and the gross structure of the molecule. G. N. Lewis

Molecular Structure Lewis description The covalent chemical bond can be thought of as a pair of electrons shared between atoms; By considering the number of electrons in the valence shell and the number of electrons in the outer atoms, we can explain the presence of lone pairs and the gross structure of the molecule in simple cases. G. N. Lewis

Molecular Structure Lewis description The Lewis description arose form an attempt to cram the observed properties of atoms in combination into a mechanically classical picture of the physical world then prevalent; in fact even classically, the structure of the atom was not explicable. G. N. Lewis http://www.chem.yale.edu/~chem125/125/history99/7BondTheory/LewisOctet/ cubicoctet.html

Molecular Structure Lewis description The Lewis description is based on the observed requirement that the atom achieves the valence shell octet associated with the noble gases - a noble gas configuration. Consider the formation of MgCl2 Mg: 1s22s22p63s2or [Ne]3s2 Cl: 1s22s22p63s23p5or [Ne]3s23p5

Molecular Structure Lewis description We know that MgCl2 is ionic and so the changes in the valence shell configurations are Mg: 1s22s22p63s2or [Ne]3s2 Mg2+: 1s22s22p6 or [Ne] Cl: 1s22s22p63s23p5or [Ne]3s23p5 Cl-: 1s22s22p63s23p6or [Ne]3s23p6 (i.e. [Ar])

Molecular Structure Lewis description We therefore account for the stability of MgCl2 through the formation of closed shell ions with noble gas configurations, namely Mg2+: 1s22s22p63s2or [Ne] and Cl-: 1s22s22p63s23p5or [Ne]3s23p6 (i.e. [Ar])

Molecular Structure Lewis description In this respect, the Lewis description of bonding is accurate, but there are major failures with molecules. Lewis described molecular structure through the idea that the atom had some inherent tetrahedral quality and that the electrons were distributed in static manner at the vertices of the tetrahedron

Molecular Structure Lewis description Lewis described molecular structure through the idea that the atom had some inherent tetrahedral structure and that the electrons were distributed in static manner at the vertices of the tetrahedron.

Molecular Structure Lewis description Molecular species therefore take structures via sharing electrons through the vertices of the tetrahedron. This naturally implies that all molecules are tetrahedral, which causes major problems for those that are not……….

Molecular Structure Lewis description Examples: BH3, CH4, NH3, OH2 and FH All these structures are based on the tetrahedron and the sharing of electrons in bonds or the presence of lone pairs at the corner of the tetrahedron.

Molecular Structure Lewis description Examples: BH3, CH4, NH3, OH2 and FH We can depict the valence shell (i.e. the shell with the highest principle quantum number) as

Molecular Structure Lewis description Examples: BH3, CH4, NH3, OH2 and FH We satisfy the open valences of these atoms with H atoms :

Molecular Structure Examples: BH3, CH4, NH3, OH2 and FH

Molecular Structure Examples: BH3, CH4, NH3, OH2 and FH The structures of the first row hydrides are not accurately predicted by the Lewis Theory of structure and bonding.

Molecular Structure VSEPR The other model for molecular structure is VSEPR. We consider a closed shell atom and we also assume that it is spherical. The structure is then determined by the number of “stereochemically active units” present in the outer shell. These stereochemically active units are the ‘lone pairs’ and the bond pairs that are formally assumed to exist in a molecule from a Lewis picture of structure and bonding.

Molecular Structure VSEPR Once we assume that bond and lone pairs exist, we introduce some other assumptions, one about structure and one about energies of interactions. The structural types that we use are based on the distribution of points on the surface of a sphere such that the distance between them is a maximum.

Molecular Structure VSEPR For two stereochemically active units, the obvious geometry is linear:

Molecular Structure VSEPR For three stereochemically active units, we form a triangular arrangement of atoms around the central atom: This geometry is termed Trigonal Planar

Molecular Structure