A Practical Guide to Gaussian Calculations
(c) 2003 C. Kemnitz
Throughout this guide blue will be used to designate typed text or filenames and green text will be used to designate menu selections.
Keeping Things Organized
You will be creating several files and the chemistry programs themselves will be creating dozens of files in each directory. It is, therefore, essential to keep everything well organized so that you can find important files quickly and do not inadvertently write over or delete an important file. Create a folder on the C drive called 352, C:\Chem352 then create a subfolder within that with your first initial and last name (e.g., C:\Chem352\ckemnitz). All of your files will be kept within this folder. The files also serve as your lab notebook for this class so they must be maintained and named in an organized fashion. You may also wish to keep a notepad handy for sketching molecules and jotting down information.
At the very least, i expect that you will create a new folder for each lab. So create four new folders immediately and call them: lab1, lab2, lab3, and lab4.
Within each lab's directory you should have a descriptive file that serves as an index and laboratory notebook for that laboratory. The file should be named, for example, _lab1_notebook.doc. This naming will keep the file at the beginning of any alphabetical listing. Use any word processor to create a file that provides a brief description of the contents of that directory. In a manner that a peer could understand, describe what kind of calculations were done, for what purpose, and at what level of theory. This file should provide the reader with a key to all abbreviations used in your naming system. It lists all jobs (see below) followed by a brief description of the results [symmetry, energy (all digits), vibrational energy, key geometric features/charges]. Many of these numbers should be copied and pasted from the output files to save time and reduce the likelihood of errors. Please copy all of the digits so that there are no rounding errors. See an example of a notebook file here.
See below for recommended naming systems.
GaussView 3.0 and Gaussian 03
User Interface. GaussView is the visual interface to Gaussian 03 (which does all the serious math). GaussView allows you to build input geometries, submit geometry optimizations, and view results.
Input vs. Output Geometries. Initially you will create an 'input geometry' which is your best guess as to what the molecule looks like. You will submit that geometry to an 'optimization routine' that will adjust the bond lengths, bond angles, and dihedrals to give you an 'output geometry.' Both of these may look quite similar on the screen but it is essential that you keep them straight, thus, they are kept in different file types by the computer and can be differentiated by their file extension.
Input geometry: filename.gjf
Output geometry: filename.log, filename.out, or filename.chk
Running a Job
Running a job requires four steps: (1) planning (2) creating an input geometry (3) submitting the job (4) analyzing the output.
(1) Planning. Although each 'job' can be a single calculation, the real job to be done often consists of a series of calculations on a single molecule, usually, with the aim of finding the best geometry at the highest level of theory. Before you begin you must have an idea of the general geometric features of your chemical structure (VSEPR) and enumerate all of the possible/likely conformations for fluxional molecules. You can only determine the global minimum on a potential energy surface if you have evaluated the energy at all of the reasonable conformations. Planning also entails using names wisely. A job will have several files associated with it and you will want to keep them all straight. At a minimum, each calculation should specify the chemical name or structure, which conformation is being probed, and the level of theory used. Here are two reasonable names for the input file of the eclipsed conformation (dihedral=0) for ethane run using the AM1 level of theory.
ethane_ecl_am1.com
or ch3ch3_0_am1.com
Update your description file, _DESCRIPTIONFILE, as you plan. Of course, it should give a key to all of your abbreviations. See an example of a description file here.
(2) Creating An Input Geometry. Input geometries are created using GaussView's builder interface. You can add atoms , rings
, or groups
by clicking on the appropriate button. The selected element has various possible attachments (initially specified as H atoms). You can select from different bonding modes for instance, from a tetracoordinate sp3 carbon to tricoordinate sp2 carbon. The selected element with its attached hydrogen atoms will appear on the screen where you click. Clicking on one of the hydrogen atoms converts it into the 'hot' atom. Once you have all of the right atoms connected properly, you can adjust the bond lengths, bond angles, and dihedral angles by using the appropriate buttons (see table below).
Buttons for Building and Evaluating Structures adjust bond length and define bond type (none, single, double, triple) adjust bond angle adjust dihedral angle measure distances, angles, and dihedral angles add a hydrogen to an atom and increase its valence delete an atom Mouse Controls
click and drag
direction control left mouse button Left-Right rotates around y-axis Up-Down rotates around x-axis right mouse button Left-Right rotates around z-axis Up-Down zoom middle mouse button All move You can either build a molecule from scratch OR modify an output file. None of the modifications you make are saved until you save the .gjf or submit the job to Gaussian. At that time it is saved as an input file. It is very important that you change the filename if you used another molecule/conformation as a template otherwise your old file will be overwritten.
Note About Symmetry. Under normal conditions Gaussian will never change your symmetry point group, so if you start with ethane exactly eclipsed, Guassian will not attempt to change the dihedral angle from 0 and the optimized geometry will be eclipsed despite the fact that this is not the optimum geometry. Gaussian, however, only recognizes symmetry when it is exact. If the two bond lengths for H2O are 1.0000 and 1.0001 they will not be considered equivalent. If symmetry is desired in the molecule select >Edit>Point Group and choose Enable Point Group Symmetry from the dialogue box (shown, right). Select the appropriate point group from the Approximate higher-order point groups drop box and click the Symmetrize button.
(3) Submitting the Job.
After an input geometry is prepared, you will need to submit it by selecting >calculate>Gaussian. GaussView is only used as interface between you and Gaussian 03. GaussView submits a job to Gaussian 03, and in some circumstances, keeps track of the job, tells you when it's done, and shows you the outcome. There are several fields that must be filled in properly for the calculation to work. The ones that we'll adjust most often are Job Type, Method, Title, and Link 0.
There are four types of jobs commonly submitted to Gaussian. Select:
>Energy: Calculates the energy at the given geometry (the molecular geometry is not altered). This is often called a 'Single Point' calculation.
>Optimization: The geometry is altered in an attempt to find a local minimum or transition state. An optimization will also give you the energy at the optimized geometry.
>Minimum: The default is to optimize to a minimum. This computation asks Gaussian to find the closest local minimum on the potential energy surface.
>Transition State: The geometry is altered in an attempt to find a transition state (a 'saddle point' on the potential energy surface). You must always start with force constants by reading them from a previous job or by computing them. Always check to make sure that the transition state that you've calculated is the one that you intend (see below).
>Frequency: The vibrational (IR) frequencies are calculated at the specified geometry. You should select 'No Raman Intensities.' NOTE: Frequency calculations are only valid when the geometry has been optimized at the same level of theory so you must open an optimized log file to begin a frequency calculation. If you know what you are doing, you can save time by asking the computation to first optimize the geometry then calculate the frequencies (>Opt+Freq).*
*Warning: The Opt+Freq results are good but subsequent calculations from the Opt+Freq log files will have extraneous keywords that will mess up future calculations. You may need to revert all keywords to the defaults when starting from an Opt+Freq geometry and re-enter all non-default selections.
Method: The 'Level of Theory' consists of a 'method' (we'll generally use Semi-Empirical AM1, Hartree-Fock, or Density Functional B3LYP) and a basis set--e.g., 6-31G(d). [Note, semi-empirical methods like AM1 have their basis set 'built in' so additional entry is not needed.] We'll talk more about interpreting this lingo in class but, for now, you'll be told what to use.
charge = 0 for neutral, 1 for +, and -1 for -.
spin multiplicity = singlet (all electrons paired), doublet for a radical (one unpaired electron), and triplet for a two unpaired electrons.
Please utilize the title field to include, at the very least, the full name of the molecule (with conformational details) and any other specifics.
The Link0 tab is optional. There are times where your professor will recommend saving a checkpoint file by clicking next to %chk= and selecting the >checkpoint file... button to save the file to a specific directory. Memory is controlled by typing an amount next to the %mem field. Some jobs, but not all of them, will run faster with more memory. For our computers 100MB is usually best.
>Submit.
When all of this information is complete, you can submit the job using the button on the bottom left. This is the first time that any information is saved. You will be prompted for a filename. Make certain that you are in the proper folder and give it an appropriate filename (as discussed earlier). This saves your input file, which should have a .gjf extension, and submits your job to Gaussian. The output file will have the same name as the input file but with a .log extension. If you'd like to edit the .gjf file as a text file before submitting it you can do so by clicking Edit.
Checking on Current Jobs. Any job, running or not, can (and should) be monitored by opening the .log file, using >file>open (see below). Unnecessary or errant jobs should be 'killed' (don't feel bad for them, they will be reborn as new jobs with happy lives). Jobs that have been submitted with the currently run session of GaussView can be killed by selecting >calculate>Current Jobs other jobs can be killed by quitting Gaussian. Some jobs take days or weeks to complete so it is important not to let them run amok.
(4) Analyzing the Output.
The output is found in the .log file. You can open an output file from GaussView by selecting >file>open and changing the job type to *.log. This will only display log files in any directory. Make sure to switch back to *.gjf when you want to view input files. You should always visually inspect the output geometry.
A job can terminate in any number of ways (listed below). To determine why a job completed you must peruse the log file as text. To view the log file select >Results>View File ...
Crash.
Sometimes there are errors or typos that cause a 'crash.' You can tell because there will be an error message in the log file, usually at the end of your log file. You should always delete these log files as soon as you know what caused the crash. If you want to keep a file but it doesn't yet contain the best geometry then change its filename to something like err_ethane_ecl_am1.log so that you don't accidentally think that the file contains an optimized geometry.
Successful Energy Calculation.
The energy is listed in Hartrees by choosing >Results>Summary.... Make sure the molecule, conformation, method, and symmetry match what you thought you were running. The absolute energy is in atomic units, often called Hartrees, and is often a large negative number (see below for conversion factor). Please round to 5 digits past the decimal. This is well beyond experimental accuracy.
Successful Geometry Optimization. There are three things you should check in an optimization log file.
(i) Visually inspect the molecule to make sure it has the structure you were interested in measuring. During optimization the molecule can move, and in some cases even changes bonding.
It may also help to see what symmetry the computer thinks your molecule is in. This is listed in >Results>Summary....
You may want to save a JPEG of the image for your lab report. To do this, find a good view of the molecule and enlarge it to occupy most of the screen. Then select >File>Save Image....
(ii) Check the convergence criteria. At the end of the log file, just before the Optimized Parameters, there should be four YESs for the four optimization criteria. Max Force, RMS Force, Max Displacement, and RMS Displacement.
(iii) Check the summary text at the end of the log file for the molecular formula, charge, multiplicity, and level of theory. Then write down (or copy/paste) the absolute energy to 5 decimal places in Hartrees.
Successful Frequency Calculation. There are two things you should check and two additional things to record when you look at a log file from a frequency calculation.
Check the Frequencies.
In GaussView select >Results>Vibrations ... to view a list of frequencies. The number of imaginary frequencies (NIMAG), represented as negative numbers here, should match the type of optimization.
NIMAG = 0 for a minimum
NIMAG = 1 for a transition state
By animating the imaginary frequency you can see that the vibrational motion represents movement along the reaction coordinate (deformation to a more stable structure).
Check the Energy.
Since frequency calculations shouldn't have changed the geometry from that optimized earlier, the energy should match that recorded for the geometry optimization.
Record the Zero-Point Vibrational Energy (ZPVE).
In the log file there will be a long list of vibrational frequencies with xyz coordinates. Look at the end of that list for Zero-point vibrational energy and write down the number.
Record the Heat Capacity (CV).
Shortly after the ZPVE comes a table that includes total CV in cal/mol-K.
Looking at Molecular Orbitals.
It is often helpful to view molecular orbitals. The easiest way to do this is to set a checkpoint file location when you first run the calculation. Make sure your checkpoint file is saved with a recognizable filename in your directory by selecting the Link0 tab, clicking next to %chk=, and selecting the >checkpoint file... button to save the file to a specific directory. When the computation is done, make sure you open the checkpoint file (*.chk). You can look at the orbitals and their energy levels in the MO window (shown below), by selecting >Edit>MOs, clicking the visualize tab, highlighting the energy levels that you'd like to see, and clicking the update... button. Orbitals cannot be printed directly from the MO window. To print an orbital, select >Results>Surfaces in the main window. If the surface has already been visualized, as described above, it will be available for display by selecting >Show Surface from the pull down menu as shown.
Running Gaussian Batch Files.
Sometimes one job is finished before there's even time to create your next input file but when the molecules are large or the level of theory is high, the computations could take considerable time. In those cases it could be expedient to create several input files and have Gaussian run them each in sequence. The benefit of this is that you can leave the computer to finish up the work and come back the next day to check the results. This method is called running files in batch. To do this, create all of your files and save them in a convenient folder. Open Gaussian and select >Utilities>Edit Batch List select add for each input file and type in the full path and filename of your input file. [Hint: It may be easier to cut and paste this information from another location. When everything is ready, save the batch file (using >File>Save As) and exit the batch editor. If the Gaussian progress message says Ready for Batch Processing Start then you may begin processing by selecting the start button 
Describing the Results and Analyzing the Data.
Usually you want the best answer in the least time. Since optimizations and frequency calculations take a long time to complete a compromise is often struck. A low level of theory (say AM1) will be used to determine the best conformation of the molecule (the one with the lowest energy). That conformation will be re-optimized at a higher level of theory, say HF/6-31G(d) and the minimum will be confirmed using a frequency calculation. A better energy (by energy, we mean electronic energy) will be determined by a 'Single Point' energy calculation at an even higher level of theory, say B3LYP/6-31+G(d,p). The format to represent this in shorthand is:
'energy method'//'optimization method'
or, for the example above, B3LYP/6-31+G(d,p)//HF/6-31G(d)
Absolute energies are of little use. For chemically interesting numbers we need to discuss relative energies. For instance, we could assess the relative energies of ethane in the staggered versus eclipsed conformations. Both molecules must have the same formula, same charge, and must be computed at the same level of theory. Relative energies, ΔE, can be converted to chemically meaningful energies using the following conversion.
1 Hartree = 627.5 kcal/mol
When we want to discuss the enthalpy of chemical reactions, for instance, the combustion of ethane, there are several computations that will be involved. The global minimum energy must be found for each molecule and a frequency calculation must be performed. First calculate the energy of reaction,
ΔErxn = [E(products) - E(reactants)](627.5 kcal/mol-Hartree)
Then convert the energy to enthalpy by adding in terms for vibrational energy and heat capacity at the specified temperature (in K).
ΔHrxn = ΔErxn + ΔZPVE + (ΔCV)(T)(1 kcal/1000 cal)
So for the combustion of ethane, one would find the minimum energy geometries of ethane, O2, H2O, and CO2 and run frequency calculations at that level. Then one might get a better energy for each molecule using a higher level of theory to calculate a good relative energy (ΔErxn ). The ZPVE and Cv corrections come from the lower level frequency calculation.
For most calculations, you cannot expect better than a 1-3 kcal/mol accuracy (semi-quantitative accuracy) but trends can often be trusted even when the numbers are only qualitative.
"
Nenhum comentário:
Postar um comentário