BBSI Computational tutorial 5-23-08 - ccbb.pitt.edu · 3 I.) Quantum Chemistry Calculations using...
Transcript of BBSI Computational tutorial 5-23-08 - ccbb.pitt.edu · 3 I.) Quantum Chemistry Calculations using...
1
Molecular Computations A BBSI Tutorial
http://www.ccbb.pitt.edu/BBSI/index.htm
By:
Jeffry D. Madura Joshua A. Plumley Sankar Manepalli Thomas J. Dick
2
Table of Contents
I.) QUANTUM CHEMISTRY CALCULATIONS USING GAUSSIAN03 AND GAUSSVIEW ............................... 3
HYDROGEN BOND STRENGTHS IN WATER, METHANOL, AND DIMETHYL ETHER
COMPLEXES ................................................................................................................... 3
CONFORMATIONAL ISOMERISM IN N-BUTANE ......................................................... 6
GLYCINE IN THE GAS PHASE AND IN WATER ............................................................ 9
II.) MOLECULAR DYNAMIC CALCULATIONS .............. 12
RAMACHANDRAN PLOT AND MOLECULAR DYNAMICS OF ALANINE DIPEPTIDE
(MOE) ........................................................................................................................ 12
DOCKING SIMULATIONS (MOE) .............................................................................. 15
III.) MOLECULAR DYNAMIC SIMULATIONS (NAMD) .... 17
SIMULATION OF BOVINE PANCREATIC TRYPSIN INHIBITOR (BPTI) IN VACUUM. 17
SIMULATION OF BOVINE PANCREATIC TRYPSIN INHIBITOR (BPTI) IN WATER ... 18
3
I.) Quantum Chemistry Calculations using Gaussian03 and Gaussview
Hydrogen Bond Strengths in Water, Methanol, and Dimethyl Ether Complexes
For the quantum mechanical calculations we will calculate the actual binding energy
between two molecules. To do this, we will use the following equation:
( ) ( ) ( )E E AB E A E BΔ = − −
This shows the binding energy (ΔE) to be equal to the energy of the complex (the two
molecules together) minus the energies of the individual components (molecules A and B
in this case). We will compute the interaction energies with the Hartree-Fock (HF)
chemical method between a series of molecules (water, methanol, and dimethyl ether)
with the 3-21G basis set. These calculations will not take that long with this level of
theory (term used to incorporate the chemical method and basis set). Then all you have to
do is some simple math. All of the energy outputs will be in hartrees. However, the unit
that is more commonly utilized is kcal/mol. Therefore report binding energies in kcal/mol
employing the following conversion, 1 kcal/mol = 627.5095 hartrees.
To perform the calculations with Gaussian03, we will build the z-matrices in
GaussView (you can also do this manually, which allows a user to control molecular
symmetry much more vigorously). Open GaussView (referred to as GV below) and you
will see methane on one of the two screens that have opened.
Click on the tab that says Carbon Tetrahedral in the middle of the screen using the
left mouse button. This will open up the Select Element window. You can choose any
element you want by clicking on the periodic table and selecting an appropriate geometry
at the bottom of the screen. Click once with the left mouse button in the blue/purple
screen to generate a carbon tetrahedral (or the functional group shown in the main
window). To replace an atom on the generated carbon tetrahedral, click on the atom in
4
the element selector window to make it “Hot”. Selecting an atom on the generated carbon
tetrahedral in the blue viewing window will be replaced by the “Hot” atom.
Example: When a carbon tetrahedral is shown in the main window and the carbon atom
is “Hot”, click once in the blue viewing window. A methane molecule should be
generated. Next, click on a hydrogen atom on the yielded methane. A ethane molecule
should be generated. One can easily see how a carbon chain may be created. Now lets try
something different. Click File → New → Create MolGroup. A new viewing window
will be opened. Next, create a methane in the new window. Now, make a hydrogen atom
“Hot” in the main window and click on a hydrogen atom on the methane in the viewing
window. See the difference from that described previously?
Tip: When two structures are within the same GV window the following shortcuts will be
useful. Place the cursor over the molecule you wish to alter. Second, press SHIFT +
ALT and the left mouse button. Lastly, move your cursor. Voila the molecule moves.
You should be able to move the corresponding structure without moving the other one. If
you wish to only rotate the structure without rotating the other one perform the previous
actions WITHOUT pressing SHIFT (in other words only press ALT).
To perform the quantum calculations, have the appropriate molecule in the
corresponding window selected. Select Calculate → Gaussian at the top of the main GV
window. In the Gaussian Calculation Setup window, click on Opt + Freq under Job type
tab; this will do a geometry optimization plus a frequency analysis. You can choose your
level of theory under the Method tab. You can also select a basis set by clicking on the
default basis set (3-21G) and changing it. Polarized and diffuse functions may be added
by the drop down menus within the next two columns next to the basis set (off to the
right). The default chemical method should be HF, which is what we will be using for
these optimizations. When you are ready to submit the calculation to Guassian, click
submit. Make a mental note of what directory the output file is saved too. Make a
mental note of what directory the output file is saved too. As the young and astute
students you are, you might be thinking to yourself, “Why is that bold and repeated
5
twice?” “Did they make a typo?” Or maybe you are just thinking, “That must be
important,” which is of course the correct assumption.
After a computation is complete you can open up the output in GV by selecting
File → Open to observe the final optimized geometry. Other results may be observed as
well. Make sure the final output GV window is selected, and then select Results →
Summary. The final electronic energy should be reported along with other useful
information such as the point group. Fill in the following two tables.
Gaussian Calculation Tables
Energy of Optimized Monomers (in hartrees):
Water ( H2O )
Methanol ( CH3OH )
Dimethyl Ether ( (CH3)2O )
Energies of Optimized Complexes (in hartrees):
Water Methanol Dimethyl ether
Water
Methanol
Dimethyl Ether
Interaction Energies:
( ) ( ) ( )E E AB E A E BΔ = − −
Remember to subtract 2 individual molecules from the complex (it can be 2 of the
same molecule). Report your final numbers in hartrees and kcal/mol (1 kcal/mol =
627.5095 hartrees).
6
Water Methanol Dimethyl ether
Water
Methanol
Dimethyl Ether
If you are diligent try this again changing the method (B3LYP, MP2, etc.) and/or
basis set (6-31G, 6-311G(d), aug-cc-pvdz, ect.). Just remember that the higher the level
of theory, the longer it takes for geometries to optimize.
These binding energies will give you the relative strengths of the hydrogen bonds
that occur within these molecules in the gas phase. Does the type of substituent play a
part in the strength of the hydrogen bond that is formed between the molecules? How
might this be explained? Think of the electronic nature of the substituent.
Conformational Isomerism in n-Butane
Here we will investigate the conformational isomers of n-butane by using
theoretical methods. To start this, we will build n-butane in GaussView and save the file
(Remember where you save it). We then will modify the z-matrix in the text input file,
in order to compute the potential energy surface associated with the C-C-C-C torsion
angle in n-butane.
7
H
HH
H
H
H
H
C
H
C
H
C
C
H
C
CH3
H
HH
CH3
H
Shown here is the anti- or trans conformation, with the C-C-C-C dihedral angle at
180°. This is only one of the naturally occurring stable structures, the other being the
gauche conformation, with a dihedral of ~ 60. 0°. We will be able to see these
conformations as we plot the dihedral angle (in degrees) vs. the relative energy.
To get started we will need to modify the z-matrix within the text file in order to
compute the electronic energy at each corresponding dihedral angle. This will be done by
identifying the dihedral of interest within the z-matrix. Open the n-butane z-matrix file
with Notepad. First, HF/3-21G(d) level of theory will be replaced with B3LYP/ 6-
31g(d). Second, the input file will need to eliminate the geometry connectivity. This is
done by eliminating the geom = connectivity command in the input deck and everything
after the last dihedral angle listed at the bottom of the z-matrix file. Geom=connectivity
must be replaced with opt=(z-matrix), to ensure the structure is optimized. Third, we
must identify the appropriate dihedral angle in which the corresponding rotational barrier
will be computed, and then alter the input accordingly. In the coordination section of the
z-matrix we see that the last carbon (C11) is bonded to atom 8 (C8), forming an angle
with atom 5 (C5), and forming a dihedral angle or torsion angle with atom 1 (C1),
represented by B10, A9, and D8, respectively. This is the dihedral angle we are interested
in (C11-C8-C5-C1). Within the z-matrix you should see variables listed after the
8
coordination input (B1, B2, … A1, A2, ... D1, D2, ...etc.). The letters B, A, and D,
represent bonds, angles, and dihedrals, respectively. Close to the end of the variable list
you should see D8 ≈ 180.0o (the variable representing the dihedral angle). Replace “D8 ≈
180.0” with “D8 0.0 s 6 30.0”. This line will set D8 equal to 180.0 and scan (s for
scan) the dihedral angle by 30.0o a total of six times. Consequently the structure will be
optimized with the dihedral angle fixed at 0.0, 30.0, 60.0 ….etc.
Now we are going to compute the potential energy surface associated with the C-
C-C-C dihedral angle. Open up the Guassian 3 which opens up a window. Go to File →
Open and open the n-butane file, which displays the contents of that file, press run which
is at the right hand corner of the window.
When the simulation is complete, select File → Open in the Guassview main
window. Select the output file to open and check the Read Intermediate Geometries box
at the bottom of the screen. You should see a scroll at the top left corner of the structure
window, allowing you to scroll through the seven output structures (one for each dihedral
angle analyzed). To determine the electronic energy for each structure, follow the
instructions given in the previous section. When the summary box is displayed you can
view the electronic energy for each structure by scrolling through the different structures
in the GV window. Convert the electronic energies that are in hartrees to kcal/mol and
subtract off the lowest energy. You can plot the relative energy vs. torsion angle in Excel
or another similar program. Also, you may visualize the potential energy surface by
clicking Results → Scan.
Fill in the following plot and turn it in with the tables filled out within this tutorial.
9
How do the different conformations affect the relative energy? Does the plot
strengthen or weaken arguments on how steric effects affect the conformational
configuration that we learn about in Organic Chemistry class?
Glycine in the Gas Phase and in Water
Glycine is the most simple amino acid, yet it has different structural forms
depending on external environmental influences, i.e. whether it is in the gas phase or in a
solution. In the gas phase, it has no charge separation and exists as Figure A below.
However, in water, it forms a zwitterion, with a deprotonation at the oxygen followed by
a protonation at the nitrogen, as shown in Figure B.
0 30 60 90 120 150 180
C-C-C-C dihedral angle (o)
Rel
ativ
e E
nerg
y (k
cal/m
ol)
10
H
N
CC
HH
O
H
OH
H
N
CC
HH
O
OH
H +
-
Figure A Figure B
In this section, we will investigate the effects of solvation on glycine and look to
see how the charge is distributed throughout the molecule. First start by building glycine
and it’s zwitterions in separate GV windows. We will optimize these at the HF/3-21+G*
level of theory with no solvation. Then optimize them again with a method of solvation
and the same level of theory, creating a four separate outputs. For the solvation method,
we will use the IEFPCM method. Fill in the Table below to see how the energies and
charge distributions are affected by the solvent.
Energy
(hartress)
Energy
(kcal/mol)
Dipole
moment
CO bond
lengths
NH bond
lengths
Carbonyl C
charge
Nitrogen
charge
Glycine
Glycine
zwitterion
Glycine
w/
solvation
Glycine
zwitterion
w/
solvation
11
What are the energies associated with solvating the glycine and the glycine
zwitterions? (Hint: Just subtract the energy of the molecule from the energy of the
solvated molecule.) Does the result support our understanding of glycine and its
zwitterion’s capabilities of being solvated, i.e. is it easier to solvate the zwitterion?
To see how the charge is distributed in the zwitterions, we will look at the
individual isolated ions found within. Build separate molecules in GaussView for the
methylammonium cation and the acetate anion. Examples are shown below in Figures C
and D.
CC
HH
O
O
H
H
N
CH
H
H
H
H-
+
Figure C Figure D
We will optimize these at the same level of theory and look at the charges on the
protonation and deprotonation sites. We will also make a comparison of the NH and CO
bond lengths, to the zwitterions. Fill in the chart below to make the comparison.
CO bond
lengths
NH bond
lengths
Carbonyl
C charge
Oxygen
charge
Nitrogen
charge
Glycine
Glycine zwitterion
Methylammonium cation x
Acetate anion x
12
Are the structures of the individual ions closer to that of the glycine or the glycine
zwitterion? Is their a full charge separation in the zwitterion based on this comparison?
How might we improve on these results?
II.) Molecular Dynamic Calculations
** Turn in the answers to the questions on a separate piece of paper.
Ramachandran Plot and Molecular Dynamics of Alanine Dipeptide (MOE)
In this Molecular Dynamics (MD) section, we will look at how a molecule
explores the energy landscape in both the gas phase and in solution. We will notice what
areas of the energy surface will be changed the most and how this affects the path of the
dipeptide in the course of the simulation.
For the MD study of conformations, we will do simulations in solution and in the
gas phase. For the MD simulations, we will look at the blocked alanine dipeptide.
1.) The contour map (Ramachandran plot) of the dihedral angles in the peptide. This will
show us which conformation(s) the dipeptide will mostly like be situated in (with respect
to the (phi/psi ) φ/ψ angles).
13
Blocked alanine dipeptide can be built in MOE by using the Edit→Build → Protein tab.
Then just click on alanine (ALA) and select both the Acetylate N-Term and Amidate C-
Term tabs at the top of the screen.
Make the φ/ψ (Ramachandran) plot for the blocked alanine dipeptide. Use the
Compute→Mechanics→Dihedral Contour Plot option. Select the φ angle (CO-N-Cα-CO
) first by clicking on the four atoms and then the ψ angle (N-Cα-CO-N) the same way. Do
this for the different force fields (Edit → Potential setup → Load ).
Go to the Pitt library website and get the following reference:
Head-Gordon, T., et. al. J. Am. Chem. Soc. 1991, 113, 5989-5997.
Compare your φ/ψ Plot to the plot found in the paper. See which force field gives the best
results. You may want to try other amino acids and compare the φ/ψ maps. What features
are the same; what features are different?
2.) To do the molecular dynamics simulation, go to Compute→ Simulations→
Dynamics (be sure to click the box to open the Database Viewer). Do the simulations
for the gas phase (with no solvation) and in solution for 100 picoseconds apiece. Set the
number of picoseconds to 100 by typing the corresponding number in the Run box. Do
the solution simulations twice, one with explicit (build a water box around dipeptide).
Draw the dipeptide for each simulation afresh as mentioned above and then simulation.
Simulation with explicit waters
To add explicit waters you have to generate water box by clicking Edit → Build→ Water
Soak. Several options will be available for you to explore. Toggle on update Periodic
Box and for this case click on Box and then adjust Box size. This will create a box
around your system of the appropriate size automatically! Then Compute the dynamics
simulation by following the steps mentioned in the previous simulation with a different
name.
14
Simulation with implicit waters
To add implicit water go to Edit →Potential setup. Under the solvation term the
Born model should be applied and. Fix hydrogens and charges and run the simulation
again.
In the main screen click Close on the right side and discard the data. In the
Database viewer, go to File → Browser (the structure should reappear in the main
screen). In the main screen, click on Measure → Dihedrals to measure the dihedrals
(both the φ and ψ angles). As you move through the simulations by advancing the frames
one or more than one at a time (you will see how in the Dynamics Animator), follow the
φ/ψ angles in the in Dihedral contour plot that was made in the beginning of this exercise.
Click on Compute → Conformations → Geometry in the database viewer window. Now
hold the shift button and select four atoms (N-C-Cα-N) in viewer. The Dihedral field in
the Conformation geometries opened panel will be shown with the selected atoms and
click Measure. Dihedral angles for the different conformers in the data base are
calculated. Click on Display → Plot and a panel opens up in the bottom half of the
database. Go to that particular column under Plot Fields. Notice how the different
conformers are plotted according to the dihedral angles calculated. Drag the mouse over
the plot for a particular conformer. This selects the conformer in the upper part of
database so that we can look at it specifically.
Does the contour map change from going from the gas phase to solution phase
(yes, you need to make another contour plot for the solution phase blocked alanine
dipeptide)? What factors do you think influences the change(s) in the energy landscape
and the path of the dipeptide through the simulation?
15
Docking Simulations (MOE)
In the Docking exercise, we will show you how to dock a drug/inhibitor (or
anything else) into the active site or the proposed (binding site) active site of a molecule.
From the earlier labs, we will show the factors that play a part in the stability of the
docked structure and how you might be able to enhance the structure to find more
favorable interactions. An example of this might be modifying a drug so it binds better in
an active site.
For the docking example, we will use carbonic anhydrase II with an inhibitor
(your choice of inhibitor when downloading (examples: PDB Id’s for a sulfonamide is
1BCD and aromatic is 1CRA ))
Open the downloaded PDB. A window will appear with some options. Leave all
the defaults and continue. Now let us prepare the protein by adding hydrogens, removing
water molecules. This can be easily done in the Sequence Editor (Click SEQ in the
upper right hand corner). Also, make the drug a separate chain by opening the Sequence
Editor selecting Edit → Split. Remove water molecules by Right Clicking on the water
chain in the Sequence Editor and selecting delete. Add hydrogens and charges by having
the substrate selected and going to Edit→Potential Setup, click on Fix hydrogens and Fix
charges. Select a force field in the Potential Control under Load. In this case, use the
MMFF94 force field. Go to Compute→Simulations→Dock. Provide the name of db to
be generated. Select receptor atoms under receptor, select Ligand atoms under Site
and Ligand atoms under Ligand. Leave default Alpha triangle under Placement as
such and choose Affinity dG under Rescoring 1. Leave the remaining two choices of
Refinement and Rescoring 2 to None and click OK at the bottom of screen.
Analyze the results by looking at the S, energy values, pocket surface, H bonds,
etc. Clicking Display → Plot allows certain columns to be plotted. In addition you may
click File → Browser and scroll through the different properties or structures (click on
the Subject box to see the properties). Open the sequence editor by clicking SEQ at the
top right hand corner. Go to selection and click on Synchronize and then select the ligand
in SEQ. This selects the ligand in the viewer (black window). Click Compute →
16
Surfaces and Maps to display the binding pocket. Select the option Selected Atoms
under Near in Surfaces and Maps and click Apply. Right now you should be thinking
“Oooooo Pretty Colors.” Modify the substrate by utilizing the Builder tool on the right
side of the screen and repeat the docking process to determine whether the new substrate
binds better or worse.
MOE allows one to see an electrostatic contour of a section so we may make an
educated guess on a modified substrate. To generate those maps, go to Compute →
Surfaces and Maps and select Electrostatic map under Surface and Selected Atoms
under Near and click apply. It generates maps in the viewer. White regions are electro
statically neutral regions whereas negative regions are shown red (acceptor) and positive
regions are shown blue (donor). Use your chemical intuition to make choices about how
to modify the substrate. Many websites offer information on the hydrophobic/
hydrophilic nature of amino acids, if that is not your area of expertise).
Write down the structure of the new compound that you have made. Does this
new molecule seem to work better or worse at binding to the Carbonic Anhydrase II?
What would be other considerations for making a “new” drug to bind in the active site
and prevent the enzyme from working properly?
17
III.) Molecular Dynamic Simulations (NAMD)
In this exercise you will simulate the protein’s motion in vaccum as well as
solvent/water by using a molecular dynamics program called NAMD. We will compare
and contrast the two simulations. A CD will be provided to you with the necessary files.
Simulation of Bovine Pancreatic Trypsin Inhibitor (bpti) in vacuum.
Use the bpti.pdb provided to you in visualization tutorial. The next step is to
create a principle structure file (psf) using the psfgen program. Make sure bpti.pdb,
bpti.pgn.txt, top_all27_prot_lipid.inp are in the same folder. Load the bpti protein in
VMD by Clicking File → New Molecule → Browse. Next, go to the directory where
the files mentioned previously are stored in the VMD command window/(black). Once
you are in that directory, type the following line in that window and press enter.
psfgen bpti.pgn.txt
If everything is done correctly, the bpti.pdb will be modified and a bpti.psf will be
generated.
Open up the command prompt (CMD) by typing cmd in run window (Start → RunI).
Go to your working directory (the directory where your files are)and type the following.
While typing the following keep in mind that [] means a single space.
namd2[]vacuum.conf []>[]bpti_vac.log . (Use this if your pc has one Processor)
namd2 []+p2[]vacuum.conf []>bpti_vac.log (Use this if your pc has two Processors)
This will take about ten minutes. If successful a number of different files named
beginning with bpti and different extensions will be created.
18
Load the bpti.pdb in VMD. Left Click on loaded bpti.pdb in the VMD main window to
highlight it and then Right click to select Load Data into molecule. Load bpti.dcd file, a
trajectory file. Click on play and see how the protein moves throughout the simulation.
Open up NAMD plot under Extensions → Analysis → NAMD plot. Load the
bpti_vac.log file created in NAMD plot and select the Energies → Total, kinetic etc.
Simulation of Bovine Pancreatic Trypsin Inhibitor (bpti) in water
Close VMD and start again or delete the previous files and do the following.
Use the psf file generated in the previous simulation. For solvating the protein
Copy the psf file generated in previous simulation to the water folder where you have the
pdb file. Load the pdb file into VMD and right click on loaded bpti.pdb and select Load
Data into molecule to load bpti.psf file. Go to your directory in the VMD command
window and type the following:
package[]require[]solvate
Solvate[]bpti.psf[]bpti.pdb[]–t[]5[]–o[]bpti_wb
This creates 5 Å3 water box around the protein and two new files are generated:
bpti_wb.psf and bpti_wb.pdb. These files will be automatically loaded into VMD and
you should see a water box surrounding the protein. If you don’t see the water box load,
delete the previously loaded bpti.pdb and bpti.psf files and load the generated
bpti_wb.pdb and right click on loaded bpti_wb.pdb and select load data into molecule
and load bpti_wb.psf file.
To simulate we now need the box dimensions in the bpti_water.config file. To
find those dimensions type the following commands in the VMD tk window which can
be found under Extensions→ Tk Console.
set everyone [atomselect top all] selects all the atoms.
19
measure minmax $everyone reports the dimensions of the box.
Subtract the minimum value from the maximum value, the result will be your box
dimensions.
measure center $everyone provides the coordinates of the center of the box.
You will be copying these dimensions into the periodic boundary conditions section of
the bpti_water_npt.conf file. The x value goes in the top row and the rest of the numbers
in that row will be zero. In the middle row everything thing will be zero except for the
middle number and all zeroes except the last number in the last row. Now copy the center
values calculated under the cell origin and save the file.
Open up the command prompt (CMD) and go to your working directory type the
following and enter
namd2[]bpti_water_npt.conf []>[]bpti_water.log . (Use this if your pc has one
Processor)
namd2 []+p2[]bpti_water_npt.conf []>[]bpti_water.log (Use this if your pc has two
Processors)
Running NAMD creates number of different files named as bpti with different extensions
Load the bpti_wb.pdb in VMD. Right click on loaded bpti_wb.pdb and select load data
into molecule and select bpti_wb_eq.dcd file, a trajectory file. Click on play and see
how the protein moves throughout the simulation.
Open up NAMD plot under Extensions → Analysis → NAMD plot. Load the created
bpti_water_npt in NAMD plot and select the energies → total, kinetic etc. The plots
can be exported to postscript viewer programs to use later.
20