View source for Mod:chem3d

See also: [[Mod:org-startup|1C comp-lab startup]],[[Mod:timetable-1C|1C Timetable]],[[mod:laptop|Laptop use]],[[mod:programs|Programs]],[[mod:organic|Module 1C Script]],[[Mod:writeup|Writing up]], [[Mod:dont_panic|Don't panic]].
==Instructions for Use of the ChemBio3D (ChemDraw) System==

The ChemBio3D/ChemDraw software can be run on the Windows Computers ''via'' invoking the  Start menu (bottom left of screen) and typing '''ChemBio3D''' into the search box. The program uniquely presents both a 2D and a 3D model, with the molecule being sketched in the former and after addition of a 3rd coordinate, the 3D model in the latter.  This makes it particularly easy to define quite complex organic molecules very quickly (you might note that the Avogadro program presents a different metaphor;  as you draw the molecule it immediately minimises the  3D energy so that bond lengths and angles get instantly corrected). 

You can '''download this software for installing on our own  Windows or Mac computer''' at [http://scistore.cambridgesoft.com/sitelicense.cfm?sid=948 this site]

If you need to '''activate''' the license for a pre-installed copy of '''ChemDraw''' you should also visit [http://scistore.cambridgesoft.com/sitelicense.cfm?sid=948 this site]
=== Setting the program defaults ===
[[Image:c3d1.jpg|thumb|left|Setting the defaults]][[Image:cb3d1.jpg|thumb|right|The main display and toolbar]]Before starting, go to '''File/Model Settings/Model Building'''. If you will be using the program for Mechanics calculation, leave the first three buttons checked (Correct building type, rectify and apply standard measurements). If you intend "importing" a file from another program as e.g. a PDB or Molfile, then deselect all these options (otherwise you may find the program eg adding hydrogens when you don't want it to). You may also find it useful to deselect these options if you are trying to rearrange the geometry of a model (the "apply standard measurements" option in particular may prevent you from moving atoms around). If in doubt, deselect all the options. Remember to "Set as default" if you want these settings to persist. Also at this stage, check the toolbars you might wish to use are displayed. There is one other important default that you will need to set relating to Gaussian calculations (see below).

=== Window layout ===
The main program display shows a  3D model on the left, a Chemdraw 2D editing pane on the right, and a results window along the bottom, together with a floating 2D editing toolbar which you can dock into the ChemDraw window if you wish. These windows can be resized as you wish. 
=== Creating a structure using the  2D editor ===
Using the Chemdraw toolbar, draw the molecule in the latter as you would, with stereochemistry etc, and as you draw, the  3D equivalent will appear on the left. If you right-mouse click in the  Chemdraw Window, other toolbars and options can be invoked. When finished, make sure the structure is "rectified", which is babble for "add hydrogens". First '''Edit/Select all''', then '''Structure/Rectify'''. ChemDraw may have added the hydrogens for you already, but it often does not.

=== Molecular  Mechanics ===
 [[Image:c3d7.jpg|thumb|left|Molecular mechanics energy]][[Image:c3d8.jpg|thumb|right|Running a molecular mechanics calculation]]To tidy the structure up use '''Calculations/MM2/MinimiseEnergy''' then '''Run'''. When complete, the sub-division of the Mechanics energy components will be seen in the status pane at the bottom. Look particularly carefully at the components of this energy, such as the bending or stretching terms to see if you can intepret the properties of your molecule. Record the total energy (in the example here, 6.5581). An alternate force field called  MMFF94 is also available (it might give slightly different results).

=== Rotating/Measuring/Copy-pasting ===
[[Image:cb3d4.jpg|thumb|left|Changing/Fixing a dihedral angle]]You can measure many properties in the  3D display window (right-mouse-click to see the options). The toolbar along the top of the  3D window contains a select (arrow),  move (hand),  rotate and zoom tool.  The arrow tool along the top edge can be used to select individual atoms (and shift-select to select multiple atoms). A mouse-over the selected atoms will reveal their properties (thus a mouse-over on four atoms will reveal the dihedral angle between 1-2 and  3-4). You can also rotate the molecule using the rotation trackball tool, and move selected atoms or molecules around using the move tool at the top. To change any measurement to a value you wish it to be, select two (three or four) atoms, and from '''Structure/Measurement/Display Dihedral measurement''' edit in the new value. If instead, you type a number into the  '''Optimal''' box, and re-run the  MM2 calculation, it will fix this value, but optimize all the rest of the geometry. Useful if  you want to obtain an approximate geometry for a transition state for example. To grab an image for your report, you can '''Edit/Select all''' the molecule, and '''Copy/as bitmap''' for pasting into eg Word.
=== Semi-empirical MOPAC Molecular orbital ===
 [[Image:cb3d2.jpg|thumb|right|Mopac calculation]][[Image:c3d6.jpg|thumb|left|Selecting the  semi-empirical parameter set]][[Image:mopac20.jpg|thumb|left|Setting the output location]]MOPAC calculations are done in a similar manner as Mechanics, but selecting  '''Calculations/Mopac interface/Minimise(Energy/Geometry)'''. You will then have to select the appropriate run time options (select the newest of the methods on offer, the PM6 or RM1 semi-empirical parameter set instead of the default  AM1).  {{fontcolor1|yellow|black|The '''Results in''' location has to be reset to the desktop, otherwise you will get an error message from V12 of the program. This does not apply if you are running  V13}}  

Semi-empirical calculations run more slowly than the mechanics mode, but it should still be interactively fast for molecules of up to around  50 atoms. Do not attempt larger molecules unless you are prepared to wait a little time (the calculation time increases as approximately the square of the number of atoms). PM6 (but not RM1) can also be used to investigate molecules containing  metals (e.g. Co etc) which cannot be run using the  mechanics methods noted above.

=== Displaying molecular surfaces/orbitals ===
You can also compute properties such as Molecular surface. In order to display  surface, you have to first calculate it! In the '''Calculations/MOPAC interface/Compute properties''' select  '''Molecular Surface'''  (assuming you have already Minimised the energy) and '''Run'''.  To display the result,  '''Surfaces/Choose Surface/Molecular Orbital'''  will display the HOMO by default. To change the displayed orbital, '''Surfaces/Molecular Orbital''' and select the one you want if its not the HOMO. To capture the orbital for your report, '''Edit/select all''', '''Edit/Copy''' and then in Word '''Edit/paste'''.

=== Ab initio/Density Functional Molecular Orbital: Batch mode ===
[[Image:cb3d5.jpg|thumb|left|Gaussian input preparation]][[Image:cb3d6.jpg|thumb|right|Gaussian options]] ''Ab initio'' Gaussian calculations are done in a similar manner ('''Calculations/Gaussian interface/Create input file''').  You will have to select the appropriate run time options of Method=DFT/B3LYP, 6-31G Basis set and Heavy atom d Polarisation functions and H-p functions  (RB3LYP/6-31G(d,p) is the shorthand for these options as shown below and is a "standard" combination often used for research-level calculations).  Save the file, adding a  .gjf (or  .com) suffix in your  H: drive or memory stick.  You will use this file (after minor editing) to submit the Gaussian job to the  '[https://scanweb.cc.imperial.ac.uk/uportal2/ Chemistry SCAN] for which detailed instructions are [[mod:scan|available here]].

===Ab initio/Density Functional Molecular Orbital: Interactive mode ===
[[Image:cb3d8.jpg|thumb|left|Gaussian total energy]][[File:G09_advanced.jpg|thumb|right|Gaussian advanced mode]]If you don't want to wait for the SCAN to run, and for '''SMALL molecules only''', you can run the calculation interactively, just as for  MM2 and MOPAC.  Be aware however that these calculations are now between  100 and  1000 times '''slower''' than e.g. MOPAC, and can take hours to finish. If you are using a HP2560p laptop, you probably do not want to have Gaussian running for more than about an hour; it might overheat! With these caveats, proceed as follows in two steps.
#Invoke '''Calculations/Gaussian Interface/Advanced Mode''' 
#Type %Mem=1GB and  %NProcShared=4 into the input template on separate lines
#Tune any other Gaussian keywords, ie  '''B3LYP/6-31G(d,p) opt freq'''
#{{fontcolor1|yellow|black|The '''Results in''' location has to be reset from the default to the desktop, otherwise you will get an error message from V12 of the program. This does not apply if you are running V13}}  
#Press '''Run''' to start the calculation. It should start a window with Gaussian 03 if you use  V12 of the program (and G09 if  V13). The status of the job is displayed along the bottom of the window. Note particularly the displayed Link number ('''L703''' etc) since you can glean some idea of the progress if the link changes periodically. Gaussian spends most of its time in L501 doing the  SCF, and L703 doing derivatives. It will probably cycle through e.g. L501 around  15-20 times, or more for a larger molecule.  Observing this cycle will give you a very rough idea of how long one the job is going to take.  If it takes more than say 10 minutes per cycle, then the total job may well run for 3 hours or so.  At this stage, you might want to abandon the calculation (press on the spinning cursor in the top tool bar) and submit instead to the  SCAN.   The final total energy (in units of Hartree; 1 Hartree= 627.5 kcal/mol,) in this example -158.471954 should be recorded in  your report.  Do not record it in kcal/mol!

===Ab initio/Density Functional Molecular Orbital: Displaying  MOs ===
Molecular orbitals (and other surfaces) can be displayed in one of two ways.  If you ran the  Gaussian job using the SCAN, the output will be a so-called '''.fchk''' file.  Double clicking this file will open  [[Mod:gaussview|Gaussview]] and you will use this program to inspect the  MOs etc.  If  your molecule is small enough for  Gaussian to be run interactively, proceed to display orbitals as you did with  MOPAC, ie '''Calculation/Gaussian Interface/Compute Properties/Molecular surface''' and then '''surfaces/Choose surface/Molecular orbitals''' to view the  HOMO, and  '''Surfaces/Select molecular orbital''' to view others. Selecting, copying and pasting into a report is just as with  MOPAC.

=== Saving the Coordinate file ===
When your calculation is complete, you should save the final coordinate file, via '''File/Save as''' invoking a file type of '''Chemical Markup language''', or '''MDL Molfile (.mol)'''. These files can then be used (e.g. with the Jmol applet) to incorporate into a Wiki page, or  it can be read back in again to most other modelling programs (the molfile is supported by Gaussview for example). 
===Archiving the output into a digital repository===

[[Image:Dspace-mod.jpg|thumb|right|Depositing an entry in  DSpace]]If you used the  SCAN for  your calculation, you can make use of a recent innovation;  the  '''Institutional digital repository'''. This is a resource for permanently archiving calculations, spectra and crystal structures. You can get a flavour of this by archiving your own calculation in the  '''SPECTRa''' digital repository. To the right of the Portal display is a link termed  '''Publish'''.  If you click on this, and the calculation is actually in a state to be published (it may for example have failed for some reason) then appropriate  ''metadata'' for the calculation are collected, and the collection deposited into the repository.  From here, it can be retrieved in future.

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See also: [[Mod:org-startup|1C comp-lab startup]],[[Mod:timetable-1C|1C Timetable]],[[mod:laptop|Laptop use]],[[mod:programs|Programs]],[[mod:organic|Module 1C Script]],[[Mod:writeup|Writing up]], [[Mod:dont_panic|Don't panic]].