Molecular Structure

Topics
3-D structure shape (location of atoms in space)
Molecular Geometry
Valence Bond Theory
Hybrid Orbitals
Multiple Bonds
VSEPR (Valence Shell Electron Pair Repulsion)

Valence Bond Theory

Overlap of atomic orbitals – is a covalent bond that joins atoms together to form a
molecule

Consider each atom to donate 1 e- to the pair which makes up a bond

Filled Orbitals

F2

2p __ __ __ __ __ __

2s __ __

1s __ __
F F

(http://www.hull.ac.uk/php/chsajb/concepts/ho_2.html)

(http://www.ausetute.com.au/lewisstr.html)

1s2 __ 1s2 __ No empty orbitals

(http://www.ausetute.com.au/lewisstr.html)
Types of Bonds

Sigma overlap between nuclei examples include: s and s s and p p and p

Pi bond overlap above and below nuclei with parallel p orbitals

Overlap of p orbitals that are perpendicular to line through nuclei

Sigma ( σ ) bond

Filled orbitals do not contribute to bonding but do contribute to size

(http://classes.yale.edu/02-03/chem220a/studyaids.html)
Pi (π ) Bond
In atoms with double or triple bonds
π Bond is weaker than σ since less overlap

Hybridization and bond formation are simultaneous process

Hybrid orbitals overlap more effectively

Electron pairs of bonds are as far away from each other as possible thus there is a lower
energy
Lennard Jones Potential

Illustrates energy that holds atoms together in a bond or molecules together in a liquid

Y axis is energy and X axis is distance between atoms or molecules

Lower energy when brought together but energy too high if pushed very close together
Most stable position is one with lowest energy

Atoms brought close together

(http://employees.csbsju.edu/hjakubowski/classes/ch331/protstructure/olunderstandconfo.html)

Hybrid Orbitals

Element Orbitals Bonds Expected Actual Bonds

Be 1s22s2 0 2
B 1s22s22px1 1 3
C 1s22s22px12py1 2 4
(http://www.platte1.k12.wy.us/Gowdy/Chemistry/chapter_13.htm)

Mixing of different orbitals to form equivalent obitals is hybridization

Be 2p __ __ __ 2p __ __ Linear

2s __ -----> sp __ __

1s __ 1s __

B 2p __ __ __ ------->
sp2 __ __ __ Trigonal Planar
2s __ ------>

1s __
C 2p __ __ __ ------------>
sp3 __ __ __ __ Tetrahedral
2s __ ------------>

1s __

Geometry differs from either isolated orbital

Energy is also different from isolated atoms

To Determine structure
1) Draw Lewis structure and find number of pairs of electrons
2) Determine electron pair geometry
3) Determine Molecular Geometry

Electron Pair Geometry can be different or same as molecular geometry (illustrated

below)

Electron Pair Geometry of CH4: Tetrahedral

Molecular Geometry of CH4: Tetrahedral

(http://cwx.prenhall.com/bookbind/pubbooks/hillchem3/medialib/media_portfolio/text_images/CH10/FG1
0_03b.JPG)

Electron Pair Geometry of NH3: Tetrahedral

Molecular Geometry of NH3: Pyramidal
(http://cwx.prenhall.com/bookbind/pubbooks/hillchem3/medialib/media_portfolio/10.html)

Electron Pair Geometry of H2O: Tetrahedral

Molecular Geometry of H2O: Bent

(http://dbhs.wvusd.k12.ca.us/webdocs/Bonding/)

Molecular Geometry (shapes)

(http://www.elmhurst.edu/~chm/vchembook/202linear.html)

(http://www.elmhurst.edu/~chm/vchembook/202linear.html)
(http://www.elmhurst.edu/~chm/vchembook/203trigplanar.html)

(http://www.elmhurst.edu/~chm/vchembook/205trigpyramid.html)

Square Planar
(http://www.up.ac.za/academic/chem/mol_geom/planar.htm)

(http://www.elmhurst.edu/~chm/vchembook/204tetrahedral.html)

(http://fia.coas.unf.edu/gchm/chime.html)

Octahedral
(http://cwx.prenhall.com/bookbind/pubbooks/hillchem3/medialib/media_portfolio/10.html)

Summary of Molecular Geometry

No. of Electron Pair No. of

Electron Geometry Pendant Molecular Example Click below to
Pairs (Bond Angle) Atoms Geometry Formula Image show rotation.

2 linear 2 linear BeH2 Show rotation

(180o)
s3 trigonal planar 3 trigonal planar CO32- Show rotation
(120o)

2 bent NO2- Show rotation

4 tetrahedral 4 tetrahedral CH4 Show rotation
(109.5o)

3 trigonal NH3 Show rotation

pyramidal
2 bent H2O Show rotation

5 trigonal 5 trigonal PCl5 Show rotation

bipyramidal bipyramidal
(90o, 120o)
4 see-saw SF4 Show rotation

3 T-shaped BrF3 Show rotation

2 linear ICl2- Show rotation

6 octahedral 6 octahedral SF6 Show rotation
(90o)

5 square BrF5 Show rotation

pyramidal
4 square planar ICl4- Show rotation

(http://www.molecules.org/VSEPR_table.html)

Multiple Bonds

Ethane
(http://www-theor.ch.cam.ac.uk/people/ross/thesis/node143.html)

Bond Angles ~ 109.5o

Valence Carbon Electrons

Ethane Carbon p __ __ __ ---> sp3 __ __ __ __ Tetrahedral

s __

Ethene Carbon p __

sp2 __ __ __ Trigonal

Ethyne (Acetylene) p __ __

sp __ __ Linear

Hybridization in Multiple Bonds

p __ __ __ p __ p __
 ------->
-------> sp2 __ __ __ or sp2 __ __ __
s __

Ethylene (Ethene)

(http://cwx.prenhall.com/bookbind/pubbooks/hillchem3/medialib/media_portfolio/10.html)

5 σ bonds
1 π bond

Ethyne (Acetylene)

p __ __ __ p __ __ p __ __
s __ sp __ __ or sp __ __

Ethyne 3-D Orbitals

(http://wps.prenhall.com/wps/media/objects/724/741576/chapter_01.html)

Bond Length (A)

1.54 Carbon to Carbon single bond
1.34 Carbon to Carbon double bond
1.20 Carbon to Carbon triple bond

Removal of Electrons
Electrons do not come off the same order they go on

Examples:

Fe 3s23p63d64s2 Fe2+ 3s23p63d6 (4s2 comes off) Fe3+ 3s23p63d5 (3d off)

Co [Ar] 4s23d7 Co2+ 3s23p63d7 Co3+ 3s23p63d6

Cu [Ar] 3d104s1 Cu+ 3s23p63d10 Cu2+ 3s23p63d9

VSEPR minimize electron repulsion

Ammonia
NH3
1s22s22px12py12pz1

(http://www.uyseg.org/greener_industry/pages/ammonia/1AmmoniaAPQ.htm)

σ bond from p orbital

H—N—H 107.3o

Could explain by sp3 hybridization because it is close to tetrahedral angle 109.5o

Water
H2O
1s22s22px22py12pz1

(http://www.hrw.com/science/si-science/chemistry/atomic_structure/molecules/02mol.html)

H—O—H 104.5o

Could explain by sp3 hybridization because it is close to tetrahedral angle 109.5o

Valence Shell Electron Pair Repulsion (VSEPR) Model

Compound Angle Bonding Pair Lone Pair

CH4 109.5o 4 0
NH3 107.3o 3 1
H2O 104.5o 2 2

Bonding Pair charge is smaller

Lone Pair charge cloud is larger so repulsion is greater

Order of Repulsion
LP—LP > LP—BP > BP—BP

Polar Molecules and Electronegativity

Bond
Ionic metal (cation) and nonmetal (anion) Na+Cl-
Pure Covalent is with identical atoms Cl—Cl

Polar Covalent is the partial transfer or uneven sharing

(http://www.teachmetuition.co.uk/Chemistry/Intermolecular/dipole.htm)

(http://faculty.njcu.edu/tpamer/gilbert-lessons/lesson5/gilbert6-4.htm)

Dipole moment is a positive and negative side

Electron pair is more toward the Cl atom

Electronegativity decides what type of bonding

Electronegativity is the measure of ability of an atom to pull an electron toward it

Basically the strength of attraction of electrons
Linus Pauling Scale

(http://www.webelements.com/webelements/properties/text/image-balls/electroneg-pauling.html)

(http://www.bcpl.net/~kdrews/properties/properties2.html)

Electronegativity
F > O > Cl ~ N > Br > I ~ C ~ S ~ Se > P
H~P

F is the most electronegative

Cs is the least electronegative
If there is more than one atom in a compound then sum up bond moments
can imagine it is like a molecular tug of war with atoms pulling electron pair

(http://cwx.prenhall.com/bookbind/pubbooks/hillchem3/medialib/media_portfolio/10.html)

But with CO2 the dipole moment for the molecule results in 0
The reason is that there are equal pull from both directions

(http://www.hull.ac.uk/php/chsajb/symmetry&spectroscopy/ho_2.html)

These diagrams show that negative (more e-) and positive side of molecules helps in
predicting reactions

In the compound H—Cl when the bond breaks the electron will go with Chlorine because
it is more electronegative
Understand Bond Strength correlates with Electronegativity difference
Compound Electronegativity Bond Energy (kJ/mol)
Difference
H—F 1.9 570
H—Cl 0.9 430
H—Br 0.7 360
H—I 0.4 300
Greater the Electronegativity Difference then stronger the bond

Representative VSEPR Structures

Orbital geometry: Describes the geometry of the orbitals, takes the nonbonding electron
pairs into account because they must be in an orbital. The steric number and the
hybridization will give the orbital geometry (electron-pair geometry). Therefore, there are
only 5 possible orbital geometries:
Octahedral (sp3d2)
Trigonal Bipyrimidal (sp3d)
Tetrahedral (sp3)
Trigonal Planar (sp2)
Linear (sp)

Molecular Geometry: uses the nonbonding electron pairs to describe the geometry of the
molecule

(http://library.tedankara.k12.tr/chemistry/vol3/Molecular%20geometry%20and%20hybridization/z94.gif)

Steps for Determining Geometry: Draw Lewis structure and find number of pairs of
electron
Determine electron pair geometry
Determine molecular geometry
Note: Electron pair geometry can be different than molecular geometry

For Example: Tetrahedral Electron geometry can have 3 different molecular geometry
(tetrahedral, pyramidal and bent)