CHAPTER 1 DESCRIPTION OF MOPAC MOPAC is a general-purpose semi-empirical molecular orbital package for the study of chemical structures and reactions. The semi-empirical Hamiltonians MNDO, MINDO/3, AM1, and PM3 are used in the electronic part of the calculation to obtain molecular orbitals, the heat of formation and its derivative with respect to molecular geometry. Using these results MOPAC calculates the vibrational spectra, thermodynamic quantities, isotopic substitution effects and force constants for molecules, radicals, ions, and polymers. For studying chemical reactions, a transition-state location routine and two transition state optimizing routines are available. For users to get the most out of the program, they must understand how the program works, how to enter data, how to interpret the results, and what to do when things go wrong. While MOPAC calls upon many concepts in quantum theory and thermodynamics and uses some fairly advanced mathematics, the user need not be familiar with these specialized topics. MOPAC is written with the non-theoretician in mind. The input data are kept as simple as possible so users can give their attention to the chemistry involved and not concern themselves with quantum and thermodynamic exotica. The simplest description of how MOPAC works is that the user creates a data-file which describes a molecular system and specifies what kind of calculations and output are desired. The user then commands MOPAC to carry out the calculation using that data-file. Finally the user extracts the desired output on the system from the output files created by MOPAC. NOTES (1) This is the "sixth edition". MOPAC has undergone a steady expansion since its first release, and users of the earlier editions are recommended to familiarize themselves with the changes which are described in this manual. If any errors are found, or if MOPAC does not perform as described, please contact Dr. James J. P. Stewart, Frank J. Seiler Research Laboratory, U.S. Air Force Academy, Colorado Springs, CO 80840-6528. (2) MOPAC runs successfully on normal CDC, Data General, DEC-3100, Gould, and Digital computers, and also on the CDC 205 and CRAY-XMP "supercomputers". The CRAY version has been partly optimized to take advantage of the CRAY architecture. Several versions exist for microcomputers such as the IBM PC-AT and XT, Zenith, etc. 1 DESCRIPTION OF MOPAC Page 2 1.1 SUMMARY OF MOPAC CAPABILITIES 1. MNDO, MINDO/3, AM1, and PM3 Hamiltonians. 2. Restricted Hartree-Fock (RHF) and Unrestricted Hartree-Fock (UHF) methods. 3. Extensive Configuration Interaction 1. 100 configurations 2. Singlets, Doublets, Triplets, Quartets, Quintets, and Sextets 3. Excited states 4. Geometry optimizations, etc., on specified states 4. Single SCF calculation 5. Geometry optimization 6. Gradient minimization 7. Transition state location 8. Reaction path coordinate calculation 9. Force constant calculation 10. Normal coordinate analysis 11. Transition dipole calculation 12. Thermodynamic properties calculation 13. Localized orbitals 14. Covalent bond orders 15. Bond analysis into sigma and pi contributions 16. One dimensional polymer calculation 17. Dynamic Reaction Coordinate calculation 18. Intrinsic Reaction Coordinate calculation - 2 - DESCRIPTION OF MOPAC Page 3 1.6 THE DATA-FILE This section is aimed at the complete novice -- someone who knows nothing at all about the structure of a MOPAC data-file. First of all, there are at most four possible types of data-files for MOPAC, but the simplest data-file is the most commonly used. Rather than define it, two examples are shown below. An explanation of the geometry definitions shown in the examples is given in the chapter "GEOMETRY SPECIFICATION". 1.6.1 Example Of Data For Ethylene Line 1 : UHF PULAY MINDO3 VECTORS DENSITY LOCAL T=300 Line 2 : EXAMPLE OF DATA FOR MOPAC Line 3 : MINDO/3 UHF CLOSED-SHELL D2D ETHYLENE Line 4a: C Line 4b: C 1.400118 1 Line 4c: H 1.098326 1 123.572063 1 Line 4d: H 1.098326 1 123.572063 1 180.000000 0 2 1 3 Line 4e: H 1.098326 1 123.572063 1 90.000000 0 1 2 3 Line 4f: H 1.098326 1 123.572063 1 270.000000 0 1 2 3 Line 5 : As can be seen, the first three lines are textual. The first line consists of keywords (here seven keywords are shown). These control the calculation. The next two lines are comments or titles. The user might want to put the name of the molecule and why it is being run on these two lines. These three lines are obligatory. If no name or comment is wanted, leave blank lines. If no keywords are specified, leave a blank line. A common error is to have a blank line before the keyword line: this error is quite tricky to find, so be careful not to have four lines before the start of the geometric data (lines 4a-4f in the example). Whatever is decided, the three lines, blank or otherwise, are obligatory. - 3 - DESCRIPTION OF MOPAC Page 4 In the example given, one line of keywords and two of documentation are shown. By use of keywords, these defaults can be changed. Modifying keywords are +, &, and SETUP. These are defined in the KEYWORDS chapter. The following table illustrates the allowed combinations: Line 1 Line 2 Line 3 Line 4 Line 5 Setup used Keys Text Text Z-matrix Z-matrix not used Keys + Keys Text Text Z-matrix not used Keys + Keys + Keys Text Text not used Keys & Keys Text Z-matrix Z-matrix not used Keys & Keys & Keys Z-matrix Z-matrix not used Keys SETUP Text Text Z-matrix Z-matrix 1 or 2 lines used Keys + Keys SETUP Text Text Z-matrix 1 line used Keys & Keys SETUP Text Z-matrix Z-matrix 1 line used No other combinations are allowed. The proposed use of the SETUP option is to allow a frequently used set of keywords to be defined by a single keyword. For example, if the default criteria are not suitable, SETUP might contain " SCFCRT=1.D-8 SHIFT=30 ITRY=600 GNORM=0.02 ANALYT " " " The order of usage of a keyword is Line 1 > Line 2 > Line 3. Line 1 > SETUP. Line 2 > SETUP. SETUP > built in default values. The next set of lines defines the geometry. In the example, the numbers are all neatly lined up; this is not necessary, but does make it easier when looking for errors in the data. The geometry is defined in lines 4a to 4f; line 5 terminates both the geometry and the data-file. Any additional data, for example symmetry data, would follow line 5. Summarizing, then, the structure for a MOPAC data-file is: Line 1: Keywords. (See chapter 2 on definitions of keywords) Line 2: Title of the calculation, e.g. the name of the molecule or ion. Line 3: Other information describing the calculation. Lines 4: Internal or cartesian coordinates (See chapter on specification of geometry) Line 5: Blank line to terminate the geometry definition. Other layouts for data-files involve additions to the simple layout. These additions occur at the end of the data-file, after line 5. The three most common additions are: (a) Symmetry data: This follows the geometric data, and is ended by a blank line. - 4 - DESCRIPTION OF MOPAC Page 5 (b) Reaction path: After all geometry and symmetry data (if any) are read in, points on the reaction coordinate are defined. (c) Saddle data: A complete second geometry is input. The second geometry follows the first geometry and symmetry data (if any). 1.6.2 Example Of Data For Polytetrahydrofuran The following example illustrates the data file for a four hour polytetrahydrofuran calculation. As you can see the layout of the data is almost the same as that for a molecule, the main difference is in the presence of the translation vector atom "Tv". Line 1 :T=4H Line 2 : POLY-TETRAHYDROFURAN (C4 H8 O)2 Line 3 : Line 4a: C 0.000000 0 0.000000 0 0.000000 0 0 0 0 Line 4b: C 1.551261 1 0.000000 0 0.000000 0 1 0 0 Line 4c: O 1.401861 1 108.919034 1 0.000000 0 2 1 0 Line 4d: C 1.401958 1 119.302489 1 -179.392581 1 3 2 1 Line 4e: C 1.551074 1 108.956238 1 179.014664 1 4 3 2 Line 4f: C 1.541928 1 113.074843 1 179.724877 1 5 4 3 Line 4g: C 1.551502 1 113.039652 1 179.525806 1 6 5 4 Line 4h: O 1.402677 1 108.663575 1 179.855864 1 7 6 5 Line 4i: C 1.402671 1 119.250433 1 -179.637345 1 8 7 6 Line 4j: C 1.552020 1 108.665746 1 -179.161900 1 9 8 7 Line 4k: XX 1.552507 1 112.659354 1 -178.914985 1 10 9 8 Line 4l: XX 1.547723 1 113.375266 1 -179.924995 1 11 10 9 Line 4m: H 1.114250 1 89.824605 1 126.911018 1 1 3 2 Line 4n: H 1.114708 1 89.909148 1 -126.650667 1 1 3 2 Line 4o: H 1.123297 1 93.602831 1 127.182594 1 2 4 3 Line 4p: H 1.123640 1 93.853406 1 -126.320187 1 2 4 3 Line 4q: H 1.123549 1 90.682924 1 126.763659 1 4 6 5 Line 4r: H 1.123417 1 90.679889 1 -127.033695 1 4 6 5 Line 4s: H 1.114352 1 90.239157 1 126.447043 1 5 7 6 Line 4t: H 1.114462 1 89.842852 1 -127.140168 1 5 7 6 Line 4u: H 1.114340 1 89.831790 1 126.653999 1 6 8 7 Line 4v: H 1.114433 1 89.753913 1 -126.926618 1 6 8 7 Line 4w: H 1.123126 1 93.644744 1 127.030541 1 7 9 8 Line 4x: H 1.123225 1 93.880969 1 -126.380511 1 7 9 8 Line 4y: H 1.123328 1 90.261019 1 127.815464 1 9 11 10 Line 4z: H 1.123227 1 91.051403 1 -125.914234 1 9 11 10 Line 4A: H 1.113970 1 90.374545 1 126.799259 1 10 12 11 Line 4B: H 1.114347 1 90.255788 1 -126.709810 1 10 12 11 Line 4C: Tv 12.299490 1 0.000000 0 0.000000 0 1 11 10 Line 5 : 0 0.000000 0 0.000000 0 0.000000 0 0 0 0 Polytetrahydrofuran has a repeat unit of (C4 H8 O)2; i.e., twice the monomer unit. This is necessary in order to allow the lattice to repeat after a translation through 12.3 Angstroms. See the section on Solid State Capability for further details. - 5 - DESCRIPTION OF MOPAC Page 6 Note the two dummy atoms on lines 4k and 4l. These are useful, but not essential, for defining the geometry. The atoms on lines 4y to 4B use these dummy atoms, as does the translation vector on line 4C. The translation vector has only the length marked for optimization. The reason for this is also explained in the Background chapter. - 6 -