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
Be
B
C
Orbitals
1s22s2
1s22s22px1
1s22s22px12py1
Bonds Expected
0
1
2
Actual Bonds
2
3
4
(http://www.platte1.k12.wy.us/Gowdy/Chemistry/chapter_13.htm)
Mixing of different orbitals to form equivalent obitals is hybridization
Be
2p __ __ __
2s __
2p __ __
-----> sp __ __
1s __
B
1s __
2p __ __ __ ------->
2s __
1s __
Linear
------>
sp2 __ __ __
Trigonal Planar
C
2p __ __ __
------------>
2s __
------------>
sp3 __ __ __ __
Tetrahedral
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
Pairs
(Bond Angle) Atoms Geometry
Click below to
Formula Image show rotation.
2
linear
(180o)
BeH2
Show rotation
s3
trigonal planar 3
(120o)
trigonal planar CO32-
Show rotation
NO2-
Show rotation
2
2
linear
bent
Example
4
5
6
tetrahedral
(109.5o)
trigonal
bipyramidal
(90o, 120o)
octahedral
(90o)
4
tetrahedral
CH4
Show rotation
3
trigonal
pyramidal
NH3
Show rotation
2
bent
H2O
Show rotation
5
trigonal
bipyramidal
PCl5
Show rotation
4
see-saw
SF4
Show rotation
3
T-shaped
BrF3
Show rotation
2
linear
ICl2-
Show rotation
6
octahedral
SF6
Show rotation
5
square
pyramidal
BrF5
Show rotation
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 __ __ __
Ethyne (Acetylene)
Trigonal
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 __
Ethyne 3-D Orbitals
sp __ __
or
sp __ __
(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
CH4
NH3
H2O
Angle
109.5o
107.3o
104.5o
Bonding Pair
4
3
2
Lone Pair
0
1
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+ClPure 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)