mopac

Perform calculations according to an input file (.mop, .dat, and .arc)

$ mopac [path/to/input_file]

$ touch test.out; echo "PM7\n#comment\n\nH 0.95506 0.05781 -0.03133\nF 1.89426 0.05781 -0.03133" > test.mop; mopac test.mop & tail [[-f|--follow]] test.out

mopac input_file.mop [output_file.out]

Typically, the program is invoked by executing the mopac binary followed by the name of the input file. Output is often directed to a specified file or standard output.

input_file.mop
    The path to the MOPAC input file, which contains all necessary keywords and molecular geometry data for the calculation.

[output_file.out]
    Optional. The path where the calculation results will be saved. If omitted, output is typically directed to standard output (stdout).

MOPAC (Molecular Orbital PACkage) is a widely used semi-empirical quantum chemistry program. It performs calculations of molecular electronic structure, properties, and reactions. Employing various semi-empirical Hamiltonians like AM1, PM3, PM6, and PM7, MOPAC offers a balance between computational accuracy and speed, making it suitable for larger molecules than typically handled by more computationally intensive ab initio methods.

Users prepare an input file containing keywords to specify calculation type (e.g., geometry optimization, single point energy) and the molecular structure. MOPAC is an essential tool in chemistry, materials science, and biochemistry for predicting molecular geometries, heats of formation, vibrational frequencies, and spectroscopic data.

MOPAC is a specialized scientific application, not a standard Linux utility command. It requires separate installation and may not be available on all systems by default.

The accuracy of results from MOPAC depends on the chosen semi-empirical Hamiltonian and its parameterization. It provides approximations to the molecular Schrödinger equation, which are generally less accurate than ab initio methods but are significantly faster for large systems.

Proper interpretation of MOPAC output requires a fundamental understanding of quantum chemistry principles.

MOPAC calculations are primarily controlled by keywords placed in the first line of the input file. These keywords dictate the type of calculation, desired output, and specific algorithms to be used. Common examples include:

• PM7: Specifies the PM7 Hamiltonian, the latest and often most accurate semi-empirical method in MOPAC.
• GEOMETRY: Instructs MOPAC to optimize the molecular geometry.
• 1SCF: Performs a single-point energy calculation without geometry optimization.
• CHARGE=n: Sets the total charge of the molecule (e.g., CHARGE=1 for a cation).
• HESSIAN: Calculates the Hessian matrix, used for vibrational frequency analysis and characterizing stationary points.
• BONDS: Requests calculation and output of bond orders.

A typical workflow for using MOPAC involves:
1. Creating an input file (.mop): This file contains the calculation keywords and the molecular structure (e.g., Cartesian coordinates or Z-matrix).
2. Running MOPAC: Executing the mopac command with the input file.
3. Analyzing output (.out): Reviewing the generated output file for optimized geometries, energies, charges, vibrational frequencies, and other calculated properties. Specialized visualization software is often used to interpret results.

MOPAC's lineage dates back to the early 1970s, with its foundational algorithms derived from earlier semi-empirical programs such as MINDO/3 and MNDO. The program was primarily developed and maintained by Dr. James J.P. Stewart, who continuously updated and expanded its capabilities.

Over decades, MOPAC has seen numerous significant revisions, including the introduction of improved semi-empirical Hamiltonians like AM1, PM3, PM6, and most recently, PM7. These updates have enhanced its accuracy and applicability to a wider range of chemical systems, solidifying its position as a staple in computational chemistry.