Download HyperChem® MOLECULAR MODELING

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HyperChem® MOLECULAR MODELING
HOWARD R. LEO, Ph.D.
INTRODUCTION
HyperChem is a very powerful program which calculates the properties of molecules. It can
also plot a number of the properties for easy visualization. Most, but not all, of the properties
that it can calculate are listed below. Those marked with an asterisk will be done in this lab.
1. CAPABILITIES

Geometry Optimization*
 Bond Lengths (BL)*
 Bond Angles*
 Dihedral Angles

Electronic Properties
 Energy of the Molecular Orbitals (MO’s)*
 Total Energy (electronic and nuclear)
 Partial Charges*
 Dipole Moment

Graphic Displays
 Multiple Visualizations of Molecular Shape*
 Visualizations of Molecular Orbitals (MO’s)*
 Charge Density
 Electrostatic Potentials
 Spin Density

Dynamic Properties
 Bond Vibrations
 Vibrational Spectrum
 Reaction Transition States

Miscellaneous Properties
 Surface Area
 Volume
 Polarizability
 Hydration Energy
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2. CALCULATION METHODS
There are three basic methods of calculation available in HyperChem®.

Molecular Mechanics – Uses a data base of force constants, which have been
determined from experimental data, to find the lowest energy geometric configuration of
a molecule. (For example, the force required to increase or decrease the H to C to F
bond angle is a known value for a variety of environments.) There are several data
bases and computational methods available.

Semi-empirical Quantum Mechanical – Uses the Schrödinger equation (THE
Fundamental Equation in quantum mechanics) with wavefunctions that have some
empirical information added to them. There are several semi-empirical methods that
have been developed.

Ab Initio (Latin for from the beginning) Quantum Mechanical – Uses the Schrödinger
equation with fundamental wavefunctions. There are a number of wavefunctions (called
basis sets), the more complicated the wavefunction, the better are the computed
properties.
3. USING THE MOUSE
The following terms describe using the mouse with HyperChem:
Point
Move (slide) the mouse so that the cursor points at
what you want to select in the HyperChem window.
L-Click
Press and release the left mouse button.
R-Click
Press and release the right mouse button.
Double-Click
L-Drag or
R-Drag
Press and release the left mouse button twice, quickly.
Hold down the left or right mouse button, and
move (slide) the cursor to a new position in the
workspace. Release the mouse button.
LR-Drag
Hold down the left and then the right mouse button,
move (slide) the cursor to a new position in the
workspace. Release the mouse button.
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4. HyperChem WINDOW
Magnify / Shrink
Menu Bar
X-Y Translate
Rotate in X-Y Plane (about Z axis)
Rotate about X and/or Y axis
Selection Tool
Drawing Tool
Calculation Method
***IMPORTANT Status Line ***
The blank area of the screen is called the WORK SPACE.
5. USING THE MENU SHORTCUT KEYS
Press Alt on the keyboard. Each of the menu commands will appear with a single underlined
letter. Press the desired letter on the keyboard to execute the command. The sub-menu
commands can be executed the same way, but without pressing the Alt key.
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Practice #1: Basic Screen Operations and Measurements

Opening an Existing File

Moving and Rotating the Molecule:

Increasing and Decreasing the Molecular Size:

Centering and Resizing the Molecule: space bar or Display → Scale to fit


Labeling the Atoms: Display → Labels → Symbol
Measuring Existing BL’s and Angles:

Using Different Visualizations: Display → Rendering
1. Open the file ethanol.hin: C:\HYPER51\SAMPLES\ORGANICS. When opened, you will see a
“stick” representation of the molecule in the WORK SPACE.
2. L-Click the X-Y MOVEMENT TOOL
, and move the molecule in the plane of the screen by
L-Dragging the tool in the Work Space (left and right for X movement. up and down for Y
movement.)
L-Click the X-Y PLANE ROTATION TOOL
, and rotate the molecule about the Z-axis. Again,
by L-Dragging the tool in the Work Space (left for counter clockwise, right for clockwise).
L-Click the OUT OF PLANE ROTATION TOOL
, and rotate the molecule about the X-axis by
L-Dragging up or down. Then rotate the molecule about the Y-axis by L-Dragging left or right.
3. L-Click the MAGNIFY / SHRINK TOOL
, and decrease the size of the molecule on the
screen by L-Dragging up, then increase it to approximately the original size by L-Dragging
down.
4. Center the molecule on the screen and resize it by pressing the space bar on the keyboard.
(Alternatively, on the menu bar select Display, then Scale to Fit.)
5. Label the atoms with their symbols. On the menu bar select Display, then Labels, then
Symbol.
6. Measure all of the bond lengths. L-Click the SELECTION TOOL
, then with the tool L-Click
the desired bond. The bond length will appear in the STATUS LINE in the very bottom left part
of the screen.
Measure the bond angles using the SELECTION TOOL
. With the tool, L-Drag from the first
atom to third atom forming the angle. The bond angle will appear in the STATUS LINE.
8. Try all six of the different visualization methods for the molecule. On the menu bar select
Display, then Renderings, then the Rendering Method Tab. When using Overlapping
Spheres, L-Click the Overlapping Spheres Tab, and turn on Shading.
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Practice #2: Drawing a Molecule and Using Model Build

Selecting a Default Atom: Double click the DRAWING TOOL

Select the desired atom from the periodic table

Use the DRAWING TOOL sketch a molecule on the screen

Use MODEL BUILD to add hydrogen atoms, and determine the approximate structure.
MODEL BUILD assigns standard bond lengths and angles to the structure. Build →
Add H & Model Build
1. Open the periodic table dialog box by Double-Clicking the DRAWING TOOL
Table dialog box appears:
. The Element
2. L-Click the desired atom (in this practice choose carbon). Be sure that Allow Ions and Explicit
Hydrogens are NOT checked. Close the Table or move it aside.
3. To place an atom on the screen, move the DRAWING TOOL
to the WORK SPACE and
L-Click. To place a second atom, move the DRAWING TOOL to another location (about two
inchs away) and L-Click again. To connect the atoms, L-Drag from one atom to the other.
Alternatively, move the DRAWING TOOL to the WORK SPACE and L-Drag from one place to
another, then release the mouse button. At this point two carbon atoms will be on the screen.
To bond another carbon atom, press the left mouse button again and L-Drag to another place
on the screen. Continue the same process until you have the desired number of atoms.
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4. To increase the number of bonds between two atoms, L-Click the existing bond.
(Alternatively, L-Drag from one atom to the other.) To decrease the number of bonds R-Click
the bonds.
5. To change the identity of an atom open the periodic table (see 1. above). Select the new
atom and then place the drawing tool
over an existing atom and L-Click.
6. To delete an atom, first go to the menu bar and choose SELECT, then ATOM. Also, make
sure that MULTIPLE SELECTIONS is off. Next, L-Click the unwanted atom with the
SELECTION TOOL . A circle will appear around the atom, press the delete key on the
keyboard.
7. Do not add hydrogen atoms to the structure. After the molecule has been sketched, the
hydrogen atoms can be added automatically using MODEL BUILD. From the menu bar select
Build, then Add H & Model Build.
Example #1
Draw NH3
1.
2.
3.
4.
5.
6.
7.
8.
Turn on the automatic labeling of atoms: Display → Labels → Symbols
Open the Periodic Table and select N as the default atom.
Place a single nitrogen atom in the WORK SPACE.
Use Model Build to add the hydrogen atoms, assign the standard bond lengths and angles,
and produce a three dimensional structure.
Rotate the molecule to make sure that all of the hydrogen atoms are present.
Display the molecule as overlapping spheres with shading: Display → Rendering →
Overlapping Spheres.
Center the molecule in the WORK SPACE: space bar
Print the molecule and label the printout. Hand it in with the experiment.
Example #2
Draw
O
║
CH3CH
1.
2.
3.
4.
5.
Reset the display rendering to sticks: Display → Rendering → Sticks
Select C as the default atom.
Draw three carbon atoms bonded with single bonds.
Change one of the end carbons to an oxygen atom.
L-Click the C to O bond to convert it from a single to a double bond.
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6. Use Model Build to add the hydrogen atoms, assign the standard bond lengths and angles,
and produce a three dimensional structure.
7. Rotate the molecule to make sure that all of the hydrogen atoms are present.
8. Display the molecule as Sticks & Dots: Display → Rendering → Sticks & Dots
9. Center the molecule in the WORK SPACE.
10. Print the molecule and label the printout. Hand it in with the experiment.
Example #3
Draw SO2
Reset the display rendering to sticks: Display → Rendering → Sticks
Select sulfur as the default atom, and place a single atom in the WORK SPACE.
Select oxygen as the new default atom.
Add two oxygen atoms to the structure. L-Drag form the S atom to about two inches away.
SO2 has resonance, so convert each of the single bonds to one bond plus a partial bond by
rapidly Double-Clicking each single bond. (A solid plus a dotted line should appear.)
6. Use Model Build to assign the standard bond lengths and angles.
7. Center the molecule in the WORK SPACE.
8. Print the molecule and label the printout. Hand it in with the experiment.
1.
2.
3.
4.
5.
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MOLECULAR MECHANICS CALCULATIONS
Molecular Mechanics calculations use a data base of force constants which have been
determined experimentally. The information includes:




The force required to stretch or compress bonds from their normal lengths.
The force required to open or close bond angles from their normal angles.
The force required to rotate about a bond.
The force of interaction between nonbonded atoms (van der Waals forces).
A molecular mechanics calculation “moves” the atoms around until it finds the lowest energy
structure for the molecule. The lowest energy state for a molecule corresponds to the optimized
geometry. For a large molecule it is possible to get caught in a localized energy minimum.
Thus the true lowest energy state of the molecule may not be found on the first attempt.
E
n
e
r
g
y
Local
Minimum
True
Minimum
Molecular Mechanics is used primarily for large molecules, since it is much faster than a
quantum mechanical calculation. In HyperChem there are four different methods: MM+,
AMBER, BIO+, and OPLS. The two most commonly used force fields are MM+ and AMBER.
There are also several algorithms for finding the lowest energy structure for the molecules. The
two most commonly use are Fletcher-Reeves and Polak-Ribiere.
SUMMARY OF MAJOR STEPS
Sketch
Model Build
Setup
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Compute
ASSIGNMENT #1: Use a Molecular Mechanics calculation to optimize the geometry, and
determine the geometric properties of the molecules below.
A) HCl
B) Cl2O
C) Cl2S
D) CO2
E) H2C=O
F) NH3
G) N(CH3)3
1. Sketch the molecule.
2. Use MODEL BUILD to assign the standard bond lengths and angles.
3. Measure the standard bond lengths and angles. Record the values on the data page, p18.
4. Setup to optimize the geometry using Molecular Mechanics.
a) From the menu bar select Setup then Molecular Mechanics
b) When the dialog box opens, select MM+
c) In the same dialog box select Options, the MM+ Options dialog box will open.
d) Under Electrostatics, select Bond dipoles. Also, under Cutoffs, select None.
5. Perform the Molecular Mechanics calculation.
a) From the menu bar select Compute then Geometry Optimization. The Molecular
Mechanics Optimization dialog box will open.
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b) If needed, change the setting to the ones above.
c) When you select OK the calculation will start. The output from the calculation will be
displayed in the STATUS LINE. The calculation is complete when “Converged=YES”.
6. Measure all of the optimized bond lengths and angles. Report the results on page 18.
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SEMI-EMPIRICAL QUANTUM MECHANICAL CALCULATIONS
Semi-empirical Quantum Mechanical Calculations uses the Schrödinger equation (THE
Fundamental Equation in quantum mechanics) with wavefunctions that have some empirical
information added to them. There are several semi-empirical methods that have been
developed. The most common methods are MNDO, AM1, PM3, and ZINDO/1
SUMMARY OF MAJOR STEPS
Sketch
Model Build
Setup
Compute
Single Point OR
Geometry Optimization
ASSIGNMENT #2: Use a Semi-empirical calculation to optimize the geometry, and
determine the properties of the molecules below.
A) HCl
C) H2O
D) CO2
E) H2C=O
F) NH3
G) NCl3
1. Sketch the molecule.
2. Use MODEL BUILD to assign the standard bond lengths and angles.
3. Measure the standard bond lengths and angles. Record the values on page 19.
4. Setup a Semi-empirical calculation to optimize the molecular geometry.
a) From the menu bar select Setup then Semi-empirical
b) When the dialog box opens, select AM1
c) In the same dialog box select Options, the Semi-empirical Options dialog box will open.
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d) Set the options to those shown above. The selections under Charge and Spin are
crucial, be sure to set them as shown.
5. Perform the Semi-empirical calculation to optimize the molecular geometry.
a) From the menu bar select Compute then Geometry Optimization. The Semi-empirical
Optimization dialog box will open.
b) If needed, change the setting to the ones above.
c) When you select OK the calculation will start. (If you get an error message, deselect
the selected atoms by L-Clicking a blank part of the WORK SPACE with the
SELECTION TOOL.) The output from the calculation will be displayed in the STATUS
LINE. The calculation is complete when “Converged=YES”.
6. Measure all of the optimized bond lengths and angles. Report the results on page 19.
7. Label the atoms with their partial charges: Display → Labels → Charge. Report the results
below.
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MOLECULAR ORBITAL CALCULATIONS
In addition to optimizing the geometry of a molecule, a semi-empirical calculation can also
determine the energy, electron occupation, and shape of the molecular orbitals. The shapes
can be plotted as a two dimensional contour, or as a three dimensional surface. The three
dimensional surface can be viewed several different ways.
SUMMARY OF MAJOR STEPS
Sketch
Model Build
Setup
Compute
Single Point
OR
Geometry Optimization
Compute
Orbitals
ASSIGNMENT #3: Use a Semi- empirical Quantum Mechanical single point calculation to
determine the MO’s of the molecules below.
A) H2
B) N2
C) F2
1. Sketch the molecule.
2. Use MODEL BUILD to assign the standard bond lengths and angles.
3. For ease of viewing, align the molecule with the X-axis: Edit → Align Molecules → X Axis.
4. Setup a Semi-empirical calculation to do a single point calculation (at the standard bond
length assigned by MODEL BUILD).
a) From the menu bar select Setup then Semi-empirical
b) When the dialog box opens, select AM1
c) In the same dialog box select Options, the Semi-empirical Options dialog box will open.
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d) Set the options to those shown above. The selections under Charge and Spin are
crucial, be sure to set them as shown.
5. Perform the Semi-empirical calculation.
a) From the menu bar select Compute then Single Point.
b) The calculation will start. (If you get an error message, deselect the selected atoms
by L-Clicking a blank part of the WORK SPACE with the SELECTION TOOL.)
The output from the calculation will be displayed in the STATUS LINE. The calculation is
complete when the menu bar selections reappear.
6. Calculate the Molecular Orbitals
a) From the menu bar select Compute then Orbitals.
b) The Orbitals dialog box will open.
c) The number of orbital levels you will see depends on the complexity of the molecule. The
MO’s that we are most interested in are those somewhat below zero energy (0 eV) and
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those somewhat above zero energy. If the energy levels are closely spaced, L-Drag a
small rectangle over the most closely spaced orbitals. This will expand the diagram, and
the MO’s will be displayed further apart.
d) Under the diagram check Labels. The electrons will be added to the diagram, and the
energy of each MO will be displayed.
e) When you L-Click any given MO energy level it will change its color to red, and its
energy will be displayed on the left side of the dialog box. (The energy is expressed in
electron volts, eV. (To put this in perspective, the energy of an electron in a single
hydrogen atom is –13.6 eV. So, it would take 13.6 eV to remove the electron completely
from a hydrogen atom.)
f) HOMO stands for highest occupied molecular orbital, and LUMO stands for lowest
unoccupied molecular orbital.
7. Plot the Molecular Orbitals
a) Only one M.O can be plotted at a time. Select the desired MO by L-Clicking it.
b) For the H2 molecule plot the bonding and antibonding orbitals using both methods:
2D Contours and 3D Isosurface. Make sure that orbital squared is not checked. For N2
and F2 plot only the 3D Isosurface.
c) Print each of the plots that you make, and on each printout record:
 the molecular formula
 the energy of the MO
 the type of MO (e.g. sppp
 indicate if it is occupied or unoccupied
Hand them in with the experiment.
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ASSIGNMENT #4: Use an Ab Initio Quantum Mechanical calculation to optimize the
geometry and determine the MO’s of the molecule below.
H2C=CH–CH=CH2
1. Sketch the molecule.
2. Use MODEL BUILD to assign the standard bond lengths and angles.
3. Setup to do an Ab Initio calculation.
a) From the menu bar select Setup then Ab Initio
b) When the dialog box opens, select the Basis Set 6-31G* for the wavefunction.
c) In the same dialog box select Options, the Ab Initio Options dialog box will open.
d) Set the options to those shown above. The selections under Charge and Spin are
crucial, be sure to set them as shown.
5. Perform the Ab Initio calculation with geometry optimization.
a) From the menu bar select Compute then Geometry Optimization. The Ab Initio
Optimization dialog box will open.
16
b) Set the options to those shown above.
`
c) Select OK and the calculation will start. (If you get an error message, deselect the
selected atoms by L-Clicking a blank part of the WORK SPACE with the
SELECTION TOOL.)
The output from the calculation will be displayed in the STATUS LINE. The calculation is
complete when Conv=YES. This calculation will take several minutes.
6. The molecule is planer. For ease of viewing the orbitals, rotate the so that you are looking at
the plane from an angle, not perpendicular.
6. Calculate the Molecular Orbitals
a) From the menu bar select Compute then Orbitals.
b) The Orbitals dialog box will open. If the energy levels are too closely spaced, L-Drag a
small rectangle over the most closely spaced orbitals. This will expand the diagram, and
the MO’s will be displayed further apart.
c) Check the Label box.
c) The important MO’s are the ones involved in the pi system. Record the energy of the
HOMO, the MO just below the HOMO (HOMO–1), the LUMO and the MO just above
the LUMO (LUMO+1).
7. Plot the MO’s
a) Plot the 3D Isosurface of: HOMO–1, HOMO, LUMO, and LUMO+1
b) Print each plot and label each with one of the above, its energy and electron occupation.
Hand them in with the experiment.
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MOLECULAR MECHANICS CALCULATIONS DATA PAGE
Model Build
A. HCl
B. Cl2O
C. Cl2S
D. CO2
E. H2C=O
F) NH3
G) N(CH3)3
MM+ Calculation
H to Cl Bond Length
__________
_________
1. Cl to O Bond Length
__________
_________
2. Cl–O–Cl Bond Angle
__________
________
1. Cl to S Bond Length
__________
_________
2. Cl–S–Cl Bond Angle
__________
_________
1. C to O Bond Length
__________
_________
2. C–O–C Bond Angle
__________
_________
1. C to O Bond Length
__________
_________
2. C to H Bond Length
__________
_________
3. H–C–H Bond Angle
__________
_________
1. N to H Bond Length
__________
_________
2. H–N–H Bond Angle
__________
_________
1. N to C Bond Length
__________
_________
2. C–N–C Bond Angle
__________
_________
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SEMI-EMPIRICAL CALCULATIONS DATA PAGE
Model Build
A) HCl
1. H to Cl Bond Length
__________
2. Partial Charges
AM1 Calculation
_________
a) H _________
b) Cl _________
B) H2O
1. H to O Bond Length
__________
_________
2. H–O–H Bond Angle
__________
_________
3. Partial Charges
a) O _________
b) H _________
C) CO2
1. C to O Bond Length
__________
_________
2. O–C–O Bond Angle
__________
_________
3. Partial Charges
a) O _________
b) C _________
D) H2C=O
1. C to O Bond Length
__________
_________
2. C to H Bond Length
__________
_________
3. H–C–H Bond Angle
__________
_________
4. Partial Charges
a) O _________
b) C _________
c) H _________
E) NH3
1. N to H Bond Length
__________
_________
2. H–N–H Bond Angle
__________
_________
3. Partial Charges
a) N _________
b) H _________
F) NCl3
1. N to Cl Bond Length
__________
_________
2. Cl–N–Cl Bond Angle
__________
_________
3. Partial Charges
a) N _________
b) Cl _________
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