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MOPAC 2002 Manual

Overview --- Features --- Input Data ---Theory --- Accuracy --- Program --- Bibliography and References

Overview of MOPAC (top)

General Description --- New Functionalities of MOPAC --- Technical, Compatibility and Other Changes --- Cooperative Development of MOPAC --- Graphical User Interfaces ---Use of MOPAC as an Educational tool --- General Description (II) ---Citation for MOPAC 2002 --- Structure of this Manual --- Figures --- Tables--- Related Programs

Features of MOPAC (top)

Geometry Optimization: General --- Constrained by definition --- Constrained by symmetry --- Energy Minimization --- Transition State location

Methods: MNDO-d --- NDDO Methods --- MINDO/3

SCF Procedures: Restricted Hartree Fock --- Unrestricted Hartree Fock --- SCF-CI

Derived Properties: Bond orders --- Charges --- Dipole moment --- Static (zero frequency) Polarizability --- Frequency dependent Non-Linear Optics

Types of Species that can be modeled: Atoms --- Molecules --- Ions --- Polymers --- Layer Systems --- Solids

Giant Molecules: Linear Scaling --- Lewis Structures --- Determining Net Charge --- Residue Sequence --- PDB input/output --- Charge on Residues Description of Electronic Structure --- Partial Geometry Optimization

Symmetry theory: Introduction --- Symmetry Labels --- Symmetrizing vibrations --- Accelerating the Calculation of Vibrations

Derived Properties: Electric Fields --- Electrostatic Potential --- Solvent effects --- Electronic Excited states --- Intersystem Crossing Vibrations --- Thermodynamics

Molecular Dynamics: Conservation of Energy --- Simulated Annealing --- Simulated heating --- Sampling --- Simulated vibrations --- Intrinsic Reaction Coordinate

General: Reaction Paths --- Saddle-Point Location --- Data checking --- Restarts --- Portability --- Program Structure --- Dynamic Memory Allocation

Validation: Algorithmic validation The Beta Test Usage Support

Acknowledgements

Contributors to MOPAC

Input Data (top)

The Data-Set --- Example of Data for Ethylene --- Overview of Data-Set

Keywords used by MOPAC

Specification of Keywords --- All Keywords --- Keywords that go together

Geometry

Geometry Specification --- Definition of Elements and Isotopes --- Optimization flags --- Internal Coordinate Definition --- Constraints --- Conversion to Cartesian Coordinates --- Translation Vector --- Gaussian Z-matrices --- Cartesian Coordinate Definition --- Protein Data Bank Format --- Conversion between Various Formats --- Examples of Coordinate Definitions --- Torsion or Dihedral Angle Coherency

Validation

To verify MOPAC

Other Programming Issues

Memory Considerations --- Program MAKPOL --- Program BZ --- Calculation of Electron DENSITY

Theory (top)

Introduction --- Semiempirical Theory --- Miscellaneous Topics --- Multi-Electron-Configuration-Interaction --- An SCF Calculation --- Localized M.O. theory --- Geometry Optimization --- Locating Transition States --- Solid State Capability --- Point Group Theory --- Precision --- Vibrations, etc. ---Thermochemistry --- DRC and IRC -- Saddle Calculation --- Solvation models --- Electrostatics

Semiempirical theory (Back to Theory)(top)

Semiempirical Theory ---Approximations used in MNDO, MINDO/3, AM1, PM3, and MNDO-d --- Basic Roothaan-Hall Equations --- Neglect of diatomic overlap integral --- Neglect of three and four center integrals --- One-center two-electron integrals --- NDDO two-electron two-center integrals --- Final Assembly of Two-Electron Two-Center Integrals --- MINDO/3 Two electron two center integrals --- The one-center one-electron integral H_mm--- The two-center one-electron integral H_mn--- Core-core repulsion integrals --- MINDO/3 modification to the core-core term --- MNDO modification to the core-core term --- AM1 and PM3 modifications to the core-core term --- The Self-Consistent Field Calculation --- Calculation of DH_f

Miscellaneous Topics in Semiempirical Theory(Back to Theory)(top)

Koopmans' Theorem --- Dipole moments --- Bond Orders --- Mulliken populations --- Localized orbitals --- Eigenvectors --- Localized M.O.s --- Localization Theory --- Oscillator Strength --- Outer Valence Green's Function --- Using ab initio derivatives --- Correction to the Peptide Linkage --- Convergence in SCF Calculation --- Causes of failure to achieve an SCF --- Use of C.I. in Reaction Path Calculations --- Sparkles --- Capped Bonds --- Algebraic Derivation of Overlap Integrals over Slater Orbitals --- Energies of Isolated Atoms --- "Size" of a molecule --- Gradients --- Reaction paths --- Grid Calculation

Multi-Electron Configuration Interaction (Back to Theory)(top)

Starting electronic configuration --- Microstates --- Permutations --- Energy of microstates --- Zero of energy used in MECI --- Construction of secular determinant --- States arising from various calculations --- Spin angular momentum --- Calculation of spin-states --- Choice of State to be Optimized --- Quantum Numbers --- Polarizability --- Franck-Condon considerations --- Definition of some C.I. Keywords --- Degenerate States --- Calculation of Spin Density

An SCF Calculation (Back to Theory)(top)

Starting density matrix --- Assembly of the starting Fock matrix --- Diagonalization of the Fock matrix --- Exercises involving eigenvectors --- Iterating density matrix --- Iterating Fock matrix --- Calculation of heat of formation

Localized Molecular Orbital Theory (Back to Theory)(top)

Geometry optimization (Back to Theory)(top)

EigenFollowing --- The BFGS function optimizer --- Optimization of one unknown --- Considerations in Geometry Optimization --- Overriding the default options

Solid state capability (Back to Theory)(top)

The Cluster --- The Madelung Problem ---Piezoelectric Effect --- Derivatives --- Charge Balanced Unit Cells --- Geometry Specification for Band Structure Calculations --- Electronic Band Structure --- Electronic Density of States --- Brillouin Zone: Generation of Band Structures --- Space-group operations

Point Group Theory (Back to Theory)(top)

Limitations --- Representation of Point Groups --- Identification of Point-Groups --- Infinite Groups --- Cubic Groups --- Other Degenerate Groups --- Abelian Groups --- Tolerance --- Orientation of the Abelian groups C_2v and D_2h --- Molecular Orbitals --- Normal Coordinates --- States

Level of Precision with MOPAC (Back to Theory)(top)

Fundamental Physical Constants --- Various precision levels --- Reasons for low precision --- How large can a gradient be and still be acceptable? --- Convergence tests in subroutine ITER --- Self-consistency test

Normal Coordinate Calculation (Back to Theory)(top)

Calculation of Vibrational Frequencies --- Calculation of the Hessian matrix --- Mechanism of the frame in FORCE calculation --- Vibrational Analysis --- Reduced masses --- Effective masses --- Travel --- Force Constants

Thermochemistry (Back to Theory)(top)

Basic Physical Constants --- Thermochemistry from ab initio MO methods --- Thermochemistry in MOPAC

Dynamic and Intrinsic Reaction Coordinates (Back to Theory)(top)

Description --- Equations used --- IRC --- General description of the DRC and IRC --- Option to allow only extrema to be output --- Keywords for use with the IRC and DRC --- Examples of DRC/IRC data --- Output format for IRC and DRC --- Test of DRC--verification of trajectory path --- The nitrogen molecule (Period of vibration ---Initial dynamics of N₂ with N-N distance = 1.094 Å --- Conservation of normal coordinate --- Rate of decay of starting mode) --- Half-Life for decay of initial mode ---DRC print options

Use of SADDLE Calculation (Back to Theory)(top)

How to escape from a hilltop --- Keyword Sequences to be Used

Polarizability and Hyperpolarizability Calculation (Back to Theory)(top)

Time-Dependent Hartree-Fock

Examples of POLAR keyword

Solvation methods (Back to Theory)(top)

COSMO --- Linear Scaling COSMO --- COSMO Keywords --- Solvent Accessible Surface --- Some hints on the use of COSMO)

Miertus-Scrocco-Tomasi Solvation Model (Outline of the MST Method --- Warnings ---Data Requirements for MST Model)

Parametric Molecular Electrostatic Potential (PMEP) (Back to Theory)(top)

2-D Electrostatic Potential Plots --- Choice of Plane to be Calculated --- Atomic Charges

Accuracy of Methods in MOPAC (top)

Protocols used in Determining Accuracy Structure of the Tables

Limitations of MNDO --- Accuracy of AM1 --- Accuracy of PM3 --- Faults and Errors in PM3 --- Faults and Errors in PM5

Average errors for various quantities for MNDO, AM1, PM3, and PM5, by element

Heats of Formation --- Bond-Lengths --- Angles --- Dipole Moments --- Ionization Potentials

Comparison of various quantities for MNDO, AM1, PM3, and PM5. These tables give results for individual systems.

Heats of formation --- Geometries --- Dipole Moments --- Ionization Potentials

Program (top)

Main geometric sequence --- Main electronic flow --- Control within MOPAC

Error messages produced by MOPAC --- Criteria --- Debugging --- Installing MOPAC --- Compiling MOPAC --- Running MOPAC --- The shut command --- Size of MOPAC --- Porting MOPAC to other platforms

Reference Heats of formation

Bibliography (top)

Elements --- Geometry --- Electronics --- General --- References

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