(Last updated May 12, 2010)

Performing Gaussian Calculations on the Linux Clusters at Lamar University

Welcome to the wonderful world of computational chemistry!!! By choosing Atari Chemistry you wont have to worry about smelling like ether at the end of the day, but you may get that oh-so-nice computer-screen tanning thing goin on! The program that you will be using is called Gaussian. The two versions that we have here are the 1998 version (Gaussian 98, or G98) and the 2003 version (Gaussian 03, or G03). There actually is a 2009 version, but we dont have that here on our clusters. Anyone who does computational research with me will learn how to use the TeraGrid, which contains Gaussian09. We currently have two different clusters in which to perform calculations. These clusters are titled CALCIUM and CARBON. CALCIUM CARBON = = Computers All Living Chaotically In Utter Mayhem Computers Arranged Randomly Between Our Nodes

Both clusters are set up to behave and perform nearly identically, with the exception that CARBON is running G98 and CALCIUM is running G03. On each one of our systems, the Gaussian program runs on a cluster of 8 processors all working together. The calculation that you ask Gaussian to perform is distributed between many processors to get the answer faster. Teamwork! To access the program, you have to understand a little about how it is set up and the hoops you have to jump through to get it there.

MASTER

NODE 1

NODE 2

NODE 3

NODE 4

NODE 5

NODE 6

NODE 7

CARBON Cluster at LU Chemistry

You can connect to either cluster through a secure shell connection, called ssh. If you have ever used telnet, then you are already somewhat familiar with this system. The difference is that the data transferred is encoded, thus the secure feature. We have set up two addresses that you can use to connect to each cluster. If it does not work, please contact Dr. Martin. carbon.lamar.edu calcium.lamar.edu

When you connect to the master node, you will be maneuvering in an operating system called Linux. Below are a few Linux commands that you will need to get around in the system. Linux Commands Command ls cd xxx cd .. mkdir xxx passwd grep xxx yyy g98l xxx.com & g03l xxx.com & ps ax kill -9 ID# pico xxx
*

Description list files and directories change directory, enters the directory named xxx go backwards (up) one directory (there is a space after the cd) make a directory called xxx in the current directory changes the current password allows you to search a file called yyy for word xxx. It will display every line that contains the word xxx without having to open the file. submits the file called xxx.com to Gaussian 98* (CARBON only) submits the file called xxx.com to Gaussian 03 (CALCIUM only) views the job queue on the cluster kills the Gaussian job currently running with the indicated ID# Opens the file named xxx to be edited

[NOTE: The first set of characters would be read as gee-ninety eight-ell and not gee-nine eighty one. Its a lower cased letter L. The l stands for Linda the type of Linux on the system.]

The Gaussian Input File The Gaussian input file can be the most intimidating part of starting calculations. The key to understanding the mix of all the numbers and letters is to understand what each line means, and what is required for a job to run. Although we have a graphical program which allows you to construct the molecule and creates the resulting input file, it is very important to understand what goes into the input file. Very often, its easier (and faster) to just edit an existing input file. Additionally, the graphical program is NOT on the cluster that Gaussian is located, which makes small changes much more difficult since the files need to be uploaded and downloaded between the server and the desktop computer on which you are working. We will slowly work through a single example. Below is the text for the com file for performing a simple optimization calculation on water. Lets break down this input file line by line. OK? Lets call this file water-1.com. _______________________________________________________________________ %chk=water-1.chk %nprocl=8 #n opt freq b3lyp/6-31* test run on water 0 O H H 1 0.143372 0.379395 -0.491211 -0.171265 0.577682 -0.631470 -0.458359 0.061859 0.063950

Now we are going to go line-by-line and discuss each item. %chk=water-1.chk The first line of the input file tells Gaussian that the name of the checkpoint file will be. The checkpoint file is like a scratch pad of all of the equations and data used in performing the calculation. The name you use for the checkpoint file should be the same as the com file. Therefore you can safely assume that I called this com file water-1.com. In some cases you may need to ask Gaussian to perform further calculations using the equations and values in the checkpoint file. %nprocl=8 This line tells Gaussian how many processors to use to perform the calculation. The more processors, the faster the calculation will be done. Since there are 7 nodes attached to the master on the CARBON cluster, there are a total of 8 processors that can be used. Here, I used all 8. If any processors are missing or not working correctly, youll have to tell the master not to look for them, and then youll have to reduce the number of processors to use. Ask Dr. Martin and hell help you if this is a problem. #n opt freq b3lyp/6-31* This line has 5 different pieces of information. Sometimes it will contain more, sometimes less. Lets go over each piece. #n This tells Gaussian to use normal output for the log file. The other option that people sometimes like is #t which stands for truncated output, or a shorter log file. As long as you know that the data you are looking for is in the log file, its your choice to use normal or truncated. opt If you want to optimize a geometry, it means that you want Gaussian to adjust the bond lengths, angles, and dihedrals to find the lowest energy conformation of the molecule (without going uphill first). The command to tell Gaussian to optimize the molecular geometry is opt. Remember that the point at which it optimizes is dependent on the starting geometry you give it. It will follow the curvature of the potential energy surface to find the first local minimum it reaches. You do not necessarily have to optimize a structure. If you just want Gaussian to calculate the energy without changing any atomic coordinates, you can do this. This type of calculation is called a single-point calculation. freq You can also ask Gaussian to calculate the vibrational frequencies of a molecule after it has been optimized. The reason for this is that the vibrational frequencies are what are observed in an IR spectrum; therefore it is a calculated IR for the molecule. The command for a frequency calculation is freq. More details on why vibrational frequencies are important will be listed below. b3lyp The first part before the slash corresponds to the level of theory. This effectively tells Gaussian how to treat the electrons (if at all) and will dictate how good your answer is, and how long it will take. In this case, this is a density functional theory calculation, or DFT. Specifically, it is Beckes 3 parameter system with a Lee, Yang, and Parr correction, B3LYP. 6-31* This is the basis set of the calculation. It indicates how many Gaussian functions you want to use to do the calculation and how to treat hydrogen atoms and polarization functions. In this case, you will be using 6 functions to describe the inner electrons, 3 functions for the middle region elections, and 1 function for the outer electrons.

It is very important to have a blank line after this section. Gaussian looks for the blank line to know that you have ended this section and it should now be looking for something else!!! test run on water This is simply a description of the job you are running. You are REQUIRED to use this space to keep the calculations straight. If I or another chemist needs to look at your data for whatever reason, we need to know what this com file is for. You will certainly have some files where all you do is change a number or two and the com files will look nearly identical. This is where you name the molecule, what you are doing to it, etc. It is very important to have a blank line after this section. Gaussian looks for the blank line to know that the description section is over!!! 0 1 This is the charge and multiplicity. If this were a cation, the charge would be 1 and 1 for an anion. The multiplicity deals with the number of electrons and whether they are paired or not. Normally, molecules are a singlet, 1. If it is a radical, the multiplicity is 2. If it is a triplet, like in a photochemical reaction or a naturally occurring triplet like molecular oxygen, the multiplicity is 3. 0.143372 0.379395 -0.491211 -0.171265 0.577682 -0.631470 -0.458359 0.061859 0.063950

O H H

This section contains the molecules Cartesian Coordinates. The units are in angstroms and the three columns represent the position of the indicated atom in the x, y, and z direction. There is another method for telling Gaussian where the atoms are located which is called a Z-matrix. The Z-matrix uses a single atom as the center of the coordinate system and all other atoms are designated by a pair of angles and a distance from the central atom in polar coordinates. (If you want to know more about Z-matrices, look it up online.) I prefer Cartesian coordinates, but as long as everything works, I have no problem with you using either one. It is very important to have a blank line after this section as well. Gaussian looks for the blank line to know that the coordinate section is over!!! If you want to type in the previous information in another program and sftp it over to the master, or if you want to type it all into a text editor in Linux, both should work fine. SFTP stands for secure file transfer protocol; its a drag-and-drop way to move files to and from the server. You can use Gaussview, Chem3D, Avagadro or another program to create your coordinate system. There are two different text editors you can use once youre connected to the cluster. The first is called vi. If you want to use this program, you are on your own. I feel its a bit cumbersome, but those who do use it swear by it. I prefer to use pico. Its fairly straightforward. The commands are listed at the bottom as a series of CTRL+[LETTER]

combinations. Youll probably need to use one of these to view the output file, the log file. Type pico xxx.log to enter pico. You can also type pico without a filename to start a new file. Once you have your com file created, start the calculation. If youre following my example, type in the following command (on CARBON): g98l water-1.com & The ampersand, &, tells the program to run the job in the background so it continues after you log off and disconnect. You must run this command in the folder where the com file is found. If everything runs OK, you should start getting lines (depending on how many nodes are operating) on your screen each saying fcflagpand this is a good thing. (This wont appear on CALCIUM) Dont worry about what this means, you just need to know that this is a sign of things working like you want it to. Every iteration that Gaussian uses will return this series of fcflapg output. The Gaussian Log File The log file contains the results of the calculation that you performed. It contains more information than you will (probably ever) need, but there are several items that you will want to look for. If the calculation that we described earlier completes normally, youll see the following output in Linux. [1] Done g98l water-1.com

There are a few ways to tell if it is well on its way or if something in wrong. If the file is only 128 lines (youll see this when you open up the log file in pico), then something probably went wrong with your input file. You may get an error something like this near the end of the log file: Error termination via Lnk1e in /usr/local/g98/l101.exe. If everything goes well, youll receive a quote at the end of the file and this message. Normal termination of Gaussian 98. If the log file is more than 128 lines long and it has not ended yet, youll want to see how far along it is. To do this, search for the word Converged?. This will let you jump to a section where you can see how close the calculation is to ending. Item Value Threshold Maximum Force 0.027773 0.000450 RMS Force 0.022669 0.000300 Maximum Displacement 0.033255 0.001800 RMS Displacement 0.033625 0.001200 Predicted change in Energy=-1.283815D-03 Converged? NO NO NO NO

This section indicates the calculated forces and the bond displacement values. When all four categories each results a calculated Value less than the Threshold then the optimization has completed. In the example above, the predicted change in energy is still quite high. See the section below for an example of a successfully converged optimization. Also, compare the predicted change in energy. The change is now very smallthis is good. Item Value Threshold Maximum Force 0.000227 0.000450 RMS Force 0.000137 0.000300 Maximum Displacement 0.000658 0.001800 RMS Displacement 0.000726 0.001200 Predicted change in Energy=-1.430195D-07 Optimization completed. -- Stationary point found. Converged? YES YES YES YES

Gaussian treats the optimization and frequency calculation as two different calculations. Each one will have its own compressed section at the end with all the most important information. Below is the data found from the optimization from our water calculation. To find this section, search for the at-sign, @.
1\1\GINC-ROUGHNECK\FOpt\RB3LYP\6-31G(d)\H2O1\MARTINCB\06-Aug-2004\0\\# N OPT FREQ B3LYP/6-31*\\test run on water\\0,1\O,0.0414303519,-0.03001 73718,-0.108374016\H,0.2790421525,0.7377868596,0.43243026\H,-0.6104849 676,-0.4976478849,0.4345618681\\Version=x86-Linux-G98RevA.7\State=1-A' \HF=-76.4089532\RMSD=1.183e-09\RMSF=7.742e-05\Dipole=-0.285144,0.20659 41,0.745883\PG=CS [SG(H2O1)]\\@

If you look hard enough, you will see most of the stuff you entered in the top part of your com file. It also gives you the optimized geometry. There are several different pieces of data that you may need from this. The first is the Hartree-Fock energy. HF=-76.4089532 This is very important. This is what you will need to compare different energies of different molecules. Cut-and-paste this number into another program for use later. Excel works great! The next piece of information is the point group, or symmetry of the molecule. PG=CS [SG(H2O1)] This tells you that the molecule has the Cs point group and has the formula H2O. Sometimes symmetry is very important. Whatever point group that results from the geometry you entered in the com file will be the point group that is retained. Therefore if you want something specific like Cs or C2v, it must be entered that way in the initial coordinates. Vibrational Frequencies As described earlier, the freq command requests a frequency calculation. Although this is technically optional, it provides a wealth of information. Sometimes, students want to perform a calculation to simply optimize a structure and then they perform a separate calculation

for an optimization followed by a frequency calculation. If you ask for a freq, you must also ask for an opt. If you are interested in viewing the data for the vibrational spectrum, search for the string Frequencies.

1 A' Frequencies -- 1713.3846 Red. masses -1.0825 Frc consts -1.8723 IR Inten -74.9388 Raman Activ -0.0000 Depolar -0.0000 Atom AN X Y Z 1 8 0.00 0.07 0.00 2 1 -0.43 -0.56 0.00 3 1 0.43 -0.56 0.00

2 A' 3727.5836 1.0454 8.5580 1.4426 0.0000 0.0000 X Y Z 0.00 0.05 0.00 0.58 -0.40 0.00 -0.58 -0.40 0.00

3 A' 3849.3113 1.0809 9.4366 19.1588 0.0000 0.0000 X Y Z 0.07 0.00 0.00 -0.55 0.44 0.00 -0.55 -0.44 0.00

The frequency (cm-1) is listed in the row labeled Frequencies and the relative intensity is listed in the row labeled IR Inten. The X, Y, Z coordinates below each frequency represents the physical displacement each atom makes to produce the vibration. Possibly the most important aspect of the vibrational calculation is the sign of the frequencies. When your calculation says Optimization completed. --Stationary point found it does NOT mean that it successfully optimized to a minimum. All it means is that it found a place where the curve of the slope (first derivative) is zero which could be a minimum or a maximum. The frequency is related to the second derivative and that will tell you more about if this stationary point is a minimum, a maximum, a saddle point, or something else. If a frequency is listed as negative, then it is really an imaginary vibration. Remember that an imaginary number is such that i2= 1. Yeah, its that kind of imaginary, but Gaussian expresses them as negative. Since the frequencies are listed in increasing wavenumbers (low to high), if the first is non-imaginary (i.e positive and real), then they all are. If all the vibrational frequencies are real, meaning that none are imaginary, then the point that Gaussian converged to is a local minimum on the potential energy surface. There is no mathematical way to determine if the local minimum calculated is actually the global maximum. The only way to feel comfortable that you have a global minimum is to do enough calculations to convince yourself that youve thoroughly explored the potential energy surface. Slight changes such as rotamers, hydrogen bonding, and anomers will all affect the energy. If one imaginary vibrational frequency was obtained, then the program has optimized to a transition state. If you are not looking for a TS, then this is bad. Take a look at the atomic displacements that correspond to the imaginary frequency to see what atoms are participating in the TS. (Use a program like GaussView that can show this graphically.) Manually change the coordinates for one or more of those atoms to try to get away from the TS. If you actually do want a TS, then you must make sure that youre actually calculating the TS you are looking for. There are numerous transition states for all sorts of potential reactions: bond breaking, bond rearranging, nucleophilic attack, bond rotations, steric interactions, etc. Again, look at the atomic displacements to see what motion the imaginary vibrational frequency is due to. To be more certain about the identity of a desired TS for a certain reaction, you may want to try an intrinsic reaction coordinate calculation, or IRC. (Look this up in a Gaussian manual or other

computational reference.) Viewing the geometry in a graphical program can help to visualize the transition states. (More to be said about this later.) NOTE: You can artificially create one or more imaginary vibrational frequencies if you request that Gaussian fixes one or more bond lengths, bond angles, or dihedral angles. Sometimes you want to fix these because the wrong bond may fragment before the rest of the molecule can optimize, so optimizing the rest first works. If you are interested in attempting this, look up the opt=modredundant keyword.

Thermal Corrections When Gaussian reports an HF energy, you must keep in mind that the energy that is reported is the bottom of the well energy. Molecules, even at zero Kelvin do not exist at this point. Therefore, Gaussian provides corrections to this number if you want the energy corrected to 0 K or to 298.15 K. These numbers are the Zero-point correction and the Thermal corrections respectively. In the section that follows, the following Hartree Fock energy was obtained for a sample calculation. HF=-230.975750 When you look in the thermochemistry section, youll see the following data.
Zero-point correction= Thermal correction to Energy= Thermal correction to Enthalpy= Thermal correction to Gibbs Free Energy= Sum of electronic and zero-point Energies= Sum of electronic and thermal Energies= Sum of electronic and thermal Enthalpies= Sum of electronic and thermal Free Energies= 0.101705 0.108320 0.109502 0.065776 -230.874045 -230.867430 -230.866248 -230.909974

If you work through the math, youll see that the last 4 numbers (sums) are where each correction is added to the HF energy. You may add the desired correction to the HF energy, or you may simply pick the appropriate sum. (See the discussion later for scaling factors.) DO NOT add more than one of these corrections to the HF. Simply add one of these numbers to the HF energy. The thermal correction already has the earlier correction(s) built in. To further understand what these numbers correspond do, you need to understand what each sum actually represents. E0 = Eelec + ZPE E = E0 + Evib + Erot + Etransl H = E + RT G = H - TS
Sum Sum Sum Sum of of of of electronic electronic electronic electronic and and and and zero-point Energies thermal Energies thermal Enthalpies thermal Free Energies

The HF energy (Eelec) is simply the electronic energy of the system at the bottom of the well. Once the zero-point energy (ZPE) is added, you get the energy of the system (E0) at zero Kelvin without any vibrational, rotational, or translational energies. For further accuracy, you can apply energy due to the vibrational (Evib), rotational (Erot), or translational (Etransl) contributions to determine the energy (E) at zero Kelvin. Remember that zero Kelvin does NOT mean that all

molecular motion has stopped, its just that all the vibrational states are at the lowest possible quantum level. For all three of the energies above (Eelec, E0, and E), no temperature has been specified or used. The enthalpy (H) is determined by applying the temperature of the system and the gas constant (R) to the energy at zero Kelvin. Finally, the Gibbs free energy (G) is determined by applying the temperature and entropy (S) to the enthalpy. If you have not specified any temperature, the temperature dependent values will be at 298.15 K. Whenever you are comparing energies, you can ONLY compare energies that were obtained using the same number of atoms with the same level of theory, the same basis set, and the same corrections. These corrections are only supplied when a frequency calculation is performed. If no frequency calculation is performed, not only are you limited to the bottom of the well energy, but you also have no supporting information to determine if you have achieved a local minimum or not. Scaling Factors Have you ever noticed that when one of your friends (or possibly a professor) tells you that something will take only a few minutes that you always need to multiply that number by five to know how much time it will actually take? Well, that can also be applied to theoretical calculations. It has been found that, depending on the basis set and level of theory, that more reliable results are found when the results are multiplied by a fudge factor, called a scaling factor. All vibrational frequencies should have this scaling factor applied. The scaling factors are often used to scale the corrections to enthalpy and entropy as well. You can either apply the scaling factor to the correction (ZPE or thermal correction) and manually add the scaled value back to the HF value or you can put the scaling factor directly into the input file and let Gaussian do the work. (See next section.) Although there are different scaling factors that can be used for the vibrational frequencies and the thermal corrections, its common practice to use the same value for both. Some of the many values that are used to calculate the thermal corrections do not actually need scaling. Therefore applying it may actually introduce errors. Allowing Gaussian to apply these corrections for us may help. Effect of Temperatures and Isotopes If you add the readisotopes option to the request for a frequency calculation in the route section, you will be able to ask for some very specific aspects in your calculation. First, in a default Gaussian calculation, all atoms are used in their default isotopic states (1H, 12C, 16O, etc.) By using this option, you have the opportunity to specify what isotopes are used in the calculation. Remember that molecular vibrations can be viewed as masses on springs. Therefore the masses (i.e. isotopes) used are actually important. Chemists may synthesize molecules with certain isotopic labels to try to determine the course of a chemical reaction. By being able to predict the difference in reaction enthalpies and vibrational frequencies due to the presence of isotopes, Gaussian calculations can help chemists know what to expect and where to look to find isotopic effects. When you use this option, you must specify the desired isotope for ALL of the atoms in the molecule. Since the frequency calculation is used to determine the zero-point and thermal corrections, this is where you can also change the temperature and pressure that would affect these corrections. By default, the temperature is at 293.15 K and 1 atmosphere of pressure. You

need to specify these values in terms of Kelvin and atmospheres when you use the readisotopes option. Finally, you may put a scaling factor into your input (com) file which will be used to scale your thermal energy corrections. Actually, this value is composed of several terms, only some of which need to be scaled, so attempting to scale everything at the end may actually remove some errors and create others. The inclusion of a scaling factor is optional. On the next page, you will find an input file for benzene that uses the readisotopes option and an explanation of how the information is arranged within the com file. Please, please, please dont enter in the information on the left side of the page. The left side is only an explanation of what is found in the com file, which is found on the right side.

Note the freq input

%chk=benzene-1.chk %nprocl=4 #n opt freq=readisotopes b3lyp/3-21g* Test on C6H6 using 'readisotopes' section 0 1 C -0.44198892 C 0.95317108 C 1.65070908 C 0.95305508 C -0.44176992 C -1.13937092 H -0.99174792 H 1.50267908 H 2.75038908 H 1.50325508 H -0.99189192 H -2.23897492

0.33149171 0.33149171 1.53924271 2.74775171 2.74767371 1.53946771 -0.62082529 -0.62102129 1.53932271 3.69989471 3.69995471 1.53965071

0.00000000 0.00000000 0.00000000 -0.00119900 -0.00167800 -0.00068200 0.00045000 0.00131500 0.00063400 -0.00125800 -0.00263100 -0.00086200

Blank line required Temp (K) & Pres.(Atm) Isotopes for above atoms in order listed (must list all) || || || || || || || || \/ Scaling Factor Blank line required at end of file

373.15 12 12 12 12 12 12 1 1 1 1 1 1 0.9804

1.0

Now that weve included this information in the input file, lets re-visit the output file. First, lets verify that the correct values were read in.
------------------- Thermochemistry ------------------Temperature 373.150 Kelvin. Pressure 1.00000 Atm. Atom 1 has atomic number 6 and mass 12.00000 Atom 2 has atomic number 6 and mass 12.00000 etc

Since Gaussian has been so kind as to allow you to put a scaling factor in the input file, it has applied this scaling factor only to the appropriate thermal terms, and then the totals have been supplied in the output file, you may simply go straight to this section in your output file to get your HF values. They do not need to have any further corrections added or scaling factors applied. Be sure that you are using the correct value for your comparisons, whether it be a change in enthalpy (Ho) or Gibbs free energy (Go).

Spin Contamination Unfortunately, we have to worry about the calculation giving us wrong numbers sometimes. (They have good intentions, honestly.) This is because some quantum numbers are common to different spin states. For example, a triplet has certain quantum numbers of 1, 0, or 1. A pentet, however, may have the corresponding quantum numbers of 2, 1, 0, -1, and 2. Since the middle 3 numbers are common for both a triplet and a pentet, the calculation may mix some higher order spin states (pentet) into the lower spin state (triplet) to get the energy lower. We just need to be careful and look for this possibility. Look for the value for the spin of the system (S2), which is indicated by the string S**2 as shown below. S**2=0.750005 The spin is determined by the following equation. S2 = S(S+1) The total unpaired electron spin is represented by the value S. Since each electron has a spin of , no unpaired electrons gives S=0, one unpaired electron gives S=1/2, and two unpaired electrons gives S=1. Therefore a singlet should have a value of S2=0, a doublet (radical) should have a value of S2=0.75, and a triplet should have a value of S2=2. Significant deviation from these values indicates that you may have significant spin contamination and the energy of the calculation may not be reliable. The result shown above was for the water radical-cation. (Charge and multiplicity: 1 2) Charge and Spin Distribution Sometimes it is useful to know how much charge or electron spin lives on each atom. All molecules exist, to some extent, as species where the charges and/or electrons are unevenly distributed throughout the molecule. Several methods exist to quantify these values. The best is probably a method called Baders Atoms in Molecules (AIM), but my experience is that the calculations often fail for the types of molecules I was studying (polycyclic heteroaromatic species). The easiest method is called the Mulliken charge distribution, which comes automatically with the output found in a log file. These are great for one thingNOTHING! Dont EVER report these values when doing calculations. Not only are the magnitudes often wrong, but they are even sometimes even in the WRONG DIRECTION! If you need charge and spin information, try a Natural Population Analysis, or NPA. To perform a NPA analysis, insert this into the line in the com file after the basis set. pop=npa When the calculation completes, extracting the values requires a little more work. Search for a section that looks like this. *************************************************** ******* Alpha spin orbitals ******* *************************************************** If you page down a little, youll then see a section that looks like this.

Summary of Natural Population Analysis: Natural Population Natural ---------------------------------------------Atom No Charge Core Valence Rydberg Total ---------------------------------------------------------------------C 1 -0.09696 0.99956 2.08961 0.00778 3.09696 C 2 -0.16541 0.99951 2.15886 0.00704 3.16541 C 3 -0.04119 0.99950 2.03405 0.00764 3.04119

A corresponding section labeled Beta spin orbitals follows. The section following this heading will look much the same as the alpha orbitals.
Summary of Natural Population Analysis: Natural Population Natural ---------------------------------------------Atom No Charge Core Valence Rydberg Total ---------------------------------------------------------------------C 1 -0.13895 0.99956 2.13188 0.00751 3.13895 C 2 0.08711 0.99950 1.90638 0.00701 2.91289 C 3 -0.09114 0.99950 2.08442 0.00722 3.09114

Obtaining the spin distribution from this data requires us to use the definition spin density: Spin density = The atoms are listed in the same order in each section. Take the number listed in the alpha section under the column labeled Total and subtract the number in the beta section for the same atom in the same column. For example, the spin density on C1 would be the following:
3.09696 - 3.13895 = -0.04199

The sum of all the spin densities of all atoms will be zero for a singlet, 1 for a doublet, and 2 for a triplet. The reason for this is the calculation actually counts the number of electrons on each atom as a function of the spin. Alpha is simply one spin state (up if you will) and the other is beta (or down) for the electrons. The NPA charges are either obtained by adding the Natural Charge numbers found in the alpha and beta sections for each atom, or you can find them a much easier way. The very beginning of the section with the NPA data, you will find a heading like the one seen below.

******************************Gaussian NBO Version 3.1****************************** N A T U R A L A T O M I C O R B I T A L A N D N A T U R A L B O N D O R B I T A L A N A L Y S I S ******************************Gaussian NBO Version 3.1******************************

Before you get to the alpha and beta sections, you will see a list of data much like described earlier in the alpha and beta sections. You will be able to tell the difference between this and the other sections by looking at the number in the column marked Total.
Summary of Natural Population Analysis: Natural Population Natural ---------------------------------------------Atom No Charge Core Valence Rydberg Total ---------------------------------------------------------------------C 1 -0.23591 1.99913 4.22150 0.01529 6.23591 C 2 -0.07830 1.99901 4.06524 0.01405 6.07830 C 3 -0.13233 1.99900 4.11847 0.01487 6.13233

Since the alpha and beta sections each account for about half of the electrons, you can expect about 3 electrons in each section for carbon (atomic number 6), for example. When the section above is examined, you can see that it is closer to 6 electrons, which what would be expected for a carbon atom. This is your clue that this section corresponds to the data you can use for the total NPA charge data. If you compare the number for C1 in this section (-0.23591) with the two separate values for the alpha (-0.09696) and beta (-0.13895) sections, you can see that getting the NPA charge data from the first section is a bit easier. Use a spreadsheet (again, like Excel) to do the math. Cutting and pasting is easy. Using Gaussian to Determine Bond Dissociation Energies, Relative Stabilities, and Other Thermodynamic Information OK, now that you can do a lot of cool things with Gaussianwhat does it all mean? One of the most common features that Gaussian is used for is a thermodynamic comparison. There are a few items that MUST be followed or else the numbers mean nothing! 1. You must compare molecules or parts of molecules that are isomers (i.e. same atoms). This means that if you want to find the homolytic bond-dissociation energy (BDE) of water, you must compare the following 3 HF values in the following way. HF(H2O) vs. HF(HO) + HF(H) You CANNOT just compare H2O and HO. The reactants and the products MUST contain the same number and the same type of atoms! You could compare the energies of water vs. water radical-cation, thats OK. The stipulation does NOT apply to electrons. Remember, its reactants minus products. (2xH and O on the left and 2xH and O on the right)

2. You must use the same level of theory and basis set for all parts calculated to be able to compare them. In the example above, we have 3 parts: water, hydroxyl radical, and hydrogen atom. If I use B3LYP/6-31G* on one of them, then I must use it on all of them or they cannot be compared. Now it is OK and common to calculate all parts with different levels of theory and different basis sets to compare the effect of changing basis sets on the final result, but each different set must be used to calculate all the parts and those parts only used with each other. For example, calculate all 3 portions with B3LYP/3-21G*. Compare the data to get a BDE for water at that level and basis set. Then, redo all the calculations (yes, all 3) with B3LYP/6-31+G**. This will allow for a comparison between 3-21G* and 6-31+G**. This is fine. 3. Any thermal corrections to the HF energy must be the same for all of the parts. If you correct water to 0 K and then correct hydroxyl radical to 298.15 K, you will be very far off in your numbers! 4. Understand that the HF number you get is not the total energy of that molecule, so you must do some comparisons to tell anything. This goes back to the same basis set and theory thing. The numbers generated are only meant for comparisons, not individual interpretations. The differences can be compared, but not the raw HF numbers. So dont report them! 5. Numbers generated should be multiplied by a scaling factor, and if used, must be applied uniformly to all calculations. This stipulation applies to both energies and vibrational frequencies. Each level of theory has its own scaling factor. The scaling factor for B3LYP is 0.9804. You may need to look up yours if you are not using B3LYP. 6. Gaussian energies are reported in HF unitsyou probably need kcal/mol. In order to get the final value in kcal/mol, you need to multiply the difference you get in HF by 627.5095. (kJ/mol are also OK, just be sure to label your units) The last page is a section of a spreadsheet that you may want to model yours after. I suggest that you save your data several ways. 1) 2) 3) Backup and save your com and log files (CD burner, flash drive, etc.) Save your worked-up data on a spreadsheet Keep a data and results summary so you can see what progress you have achieved this can also serve as a checklist of what still needs to be done

Name LF H2LF LFN10 LFN3 LFMe 1H-LF 5H-LF H2LFN10 H2LFN3 H2LFMe 2OH-LF 4OH-LF 2OH-H2LF 4OH-H2LF LC LF rad anion 1Me-LF 5Me-LF 1Me-5H-LF 1H-5Me-LF 4'Me-LF 4'Me-H2LF 10'Me-LF 2MeO-LF 4MeO-LF LF-triplet 10'H-LF 4'H-LF pCresol pCresol-t pCresol-radcat O-pCresol Me-pCresol 2C-pCresol Indole Indole-N1 Indole-C2 Indole-C3 Indole-radcat Methane Ethane Methyl. H. H2 proton iPrOH iPrOH-radical EtOH EtOH-radical MeOH MeOH-radical 1H-5Me-LF 1Me-5H-LF 1H-10'Me-LF 1Me-10'H-LF 4'H-5Me-LF 4'Me-5H-LF

B3LYP/6-31G* HF ZPE Corr. -872.1146108 0.240933 -873.3148918 0.263874 -832.1524257 0.198424 -871.4234129 0.22565 -871.4554687 0.226724 -872.6977468 0.251301 -872.7124263 0.252239 -833.4169679 0.22385 -872.6716597 0.250778 -872.6632743 0.250642 -872.6915072 0.251274 -872.6965921 0.251655 -873.8236793 0.27254 -873.8395157 0.271756 -832.8251188 0.212849 -872.1687017 0.23806 -911.9995504 0.279992 -912.0122752 0.280869 -912.6230423 0.292405 -912.6167785 0.292054 -911.9884775 0.278659 -913.1835542 0.302786 -911.9465719 0.277117 -911.9977265 0.279506 -911.9909043 0.279476 -872.0426689 0.237653 -872.629179 0.249117 -872.6721265 0.250619 -346.7822458 0.132357 -346.6352011 0.130799 -346.5004696 0.132293 -346.1477831 0.119362 -346.131849 0.119046 -346.091712 0.119378 -363.8166883 0.129926 -363.1666474 0.116216 -363.1187382 0.116405 -363.1181496 0.117129 -363.5497007 0.130317 -40.5183838 0.045228 -79.8304238 0.075264 -39.8382921 0.029832 -0.5002728 0 -1.1754824 0.010145 0 0 -194.3533175 0.108527 -193.6979751 0.094596 -155.0338009 0.080318 -154.3753608 0.066295 -115.7144048 0.051471 -115.0504625 0.037157 -912.6167785 0.292054 -912.6230423 0.292405 -912.6132863 0.291771 -912.6046193 0.292304 -912.6153632 0.292859 -912.6319078 0.292227

Corr. & Scaled -854.7849537 -855.9392179 -815.6477033 -854.1222867 -854.1526613 -855.3464955 -855.3599676 -816.8625328 -855.3214324 -855.3133447 -855.3404046 -855.3450163 -856.429537 -856.4458316 -816.2930693 -854.8408011 -893.8498551 -893.8614706 -894.4489568 -894.4431599 -893.8403061 -894.9883051 -893.8007336 -893.8485434 -893.8418843 -854.7176376 -855.2814128 -855.322046 -339.855551 -339.7129158 -339.5793603 -339.246264 -339.2309521 -339.1912763 -356.5585018 -355.9346429 -355.8874875 -355.8862006 -356.2963638 -39.67988195 -78.19195867 -39.02821428 -0.490467453 -1.142496787 0 -190.4375926 -189.8087529 -151.9163946 -151.2846081 -113.3959403 -112.7590447 -894.4431599 -894.4489568 -894.4400136 -894.4309939 -894.4409831 -894.4578231

Rxn LF + H2 --> H2LF LF + methyl --> LFN3 + methane LF + methyl --> LFMe + methane LF + methyl --> LFN10 + ethane LF + H --> 1H-LF LF + H --> 5H-LF LFN3 + H2 --> H2LFN3 LFN10 + H2 --> H2LFN10 H2LF + methyl --> 1H-LF + methane H2LF + methyl --> 5H-LF + methane H2LF + methyl --> H2LFN10 + ethane H2LF + methyl --> H2LFMe + methane H2LF + methyl --> H2LFN3 + methane methane --> methyl + H ethane --> methyl + methyl LF + H --> 2OH-LF LF + H --> 4OH-LF H2LF + H --> 2OH-H2LF H2LF + H --> 4OH-H2LF LF + methane --> LC + ethane LF + e- --> LF-rad-anion LF + methyl --> 1Me-LF LF + methyl --> 5Me-LF LF + methane --> 1Me-5H-LF LF + methane --> 1H-5Me-LF LF --> LF-triplet LF-triplet + e- --> LF-rad-anion LF-t + H. --> 5H-LF pCresol --> O-pCresol + H. pCresol --> Me-pCresol + H. pCresol --> 2C-pCresol + H. pCresol-radcat --> O-pCresol + H+ pCresol-radcat --> Me-pCresol + H+ pCresol-radcat --> 2C-pCresol + H+ pCresol --> pCresol-radcat + eIndole --> Indole-N1 + H. Indole --> Indole-C2 + H. Indole --> Indole-C3 + H. Indole-radcat --> Indole-N1 + H+ Indole-radcat --> Indole-C2 + H+ Indole-radcat --> Indole-C3 + H+ Indole --> Indole-radcat + ehydrogen --> proton + e-

DH(rxn) (kcal/mol) -7.38 6.90 -12.16 -16.63 -44.60 -53.05 -35.55 -45.39 -36.99 -45.44 -54.63 -16.19 -21.26 101.15 85.05 -40.78 -43.67 0.09 -10.13 -12.67 -35.04 -23.02 -30.31 9.96 13.60 42.24 -77.29 -95.30 74.56 84.17 109.07 209.02 218.63 243.53 173.31 83.70 113.29 114.10 226.98 256.57 257.38 164.49 -307.77

LF-triplet + iPrOH --> 5H-LF + iPrOH-radical LF-triplet + EtOH --> 5H-LF + EtOH-radical LF-triplet + MeOH --> 5H-LF + MeOH-radical iPrOH --> iPrOH-radical + H. EtOH --> EtOH-radical + H. MeOH --> MeOH-radical + H. 2(1H-LF) --> H2LF + LF 2(5H-LF) --> H2LF + LF

-8.47 -6.62 -3.41 86.83 88.68 91.89 -19.57 -2.66

LF-radanion + indole-radcat --> 1H-LF + indole-N1-90.34 LF-radanion + indole-radcat --> 2OH-LF + indole-N1 -86.52