User Manual

Michael J. S. Dewar

Andrew J. Holder

Roy D. Dennington, II

Daniel A. Liotard

Donald G. Truhlar

Todd A. Keith

John M. Millam

C. David Harris

Table of Contents

Conventions Used in This Manual
Preface to AMPAC™ 4 Manual
Preface to AMPAC™ 5 Manual
Preface to AMPAC™ 7 Manual
Preface to AMPAC™ 8 Manual
Preface to AMPAC™ 9 Manual
Preface to AMPAC™ 10 Manual
I. AMPAC 10 User Guide
1. Introduction
2. Special Features of AMPAC
3. Semiempirical Methods and Parameters
4. Computational Procedures
5. Presenting Input to the Program
6. Keywords
7. Sparse Matrix Methods
8. CHN Methods
9. Eigenvector Following
10. Electrostatic Potential
11. Configuration Interaction
12. Polarizability Methods
13. Simulated Annealing
14. COSMO Solvation Model
15. AMSOL Model Module
16. Package Administration
17. References
II. AMPAC 10 Examples
18. A Typical Calculation
19. A Large Molecule using Sparse Matrices (SPARSE, PSOLVE)
20. Analyzing the Lewis Dot Structure of a Molecule (LEWIS)
21. A Simple Example of Using Configuration Interaction
22. Solvation (COSMO, SM5.2, SM5C)
23. Cartesian Frequencies and Thermodynamics (FORCE)
24. Internal Coordinate Frequencies and Gradients (LTRD)
25. One-Dimensional Reaction Pathway
26. Two-Dimensional Grid Search
27. Finding a Specific Transition State (CHN)
28. PATH Calculation with Transition Vector
29. Intrinsic Reaction Coordinate (IRC) Calculation
30. Simulated Annealing Search for Multiple Minima (ANNEAL)
31. Electrostatic Potential Charges (ESP)
32. Natural Bond Orbital Analysis (NBO)
33. Polarizability (KPOLAR, APOLAR)
34. Use of Partial Charge Sparkles
III. AMPAC 10 User Reference
A. Keyword Reference
B. Utilities
C. Error Messages
D. Data Files
E. Debugging
F. Obsolete Keywords

List of Figures

4.1. Potential energy along a reaction coordinate
4.2. Steps for proper refinement and confirmation of a transition state
4.3. Cyclooctatetraene bathtub conformation
4.4. Cyclooctatetraene planar geometry
5.1. Bond Lengths and Bond Angle for Water
5.2. Newman Projection Showing Dihedral Angle Definition
5.3. Examples of dihedral angle definitions: Methanol
5.4. Examples of dihedral angle definitions: Ethene
5.5. A z-matrix for acetylene using dummy atoms
5.6. A z-matrix for benzene
5.7. A z-matrix for benzene using a dummy atom
14.1. Schematic representation of the Solvent Accessible Surface (SAS)
26.1. Inversion of 1,5-hexadiene
30.1. Example of a Relatively Rigid System
30.2. Trans-minimum
30.3. Cis-minimum
34.1. Water molecule polarized by two sparkles.
A.1. C.I. Active Space Definition

List of Tables

1.1. Information Available from Computational Methods
3.1. MINDO3 Atom Pair Parameters
3.2. Elemental Parameter Sets for all methods (except MINDO3)
3.3. Average Errors for Various Properties for H, C, N, O, P, S, F, Cl, Br and I (kcal/mol)
3.4. Average unsigned errors in ΔHf for various sets of elements (kcal/mol)
4.1. Default Values of SCFCRT
5.1. Optimization Flags
5.2. Sparkles
5.3. Section Markers for Extra Input Data
5.4. Symmetry Functions
19.1. Effect of the sparse matrix threshold
21.1. Possible microstates with 2 CI-active MOs
34.1. Effect of presence of sparkles
A.1. Symmetry Numbers