AMPAC™ 9 User Manual

AMPAC™
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

Copyright © 1992-2009 Semichem, Inc. All rights reserved.

Table of Contents

Contributors

Abbreviations

Conventions Used in This Manual

Preface to AMPAC™ 4.0 Manual

Preface to AMPAC™ 5.0 Manual

Preface to AMPAC™ 7.0 Manual

Preface to AMPAC™ 8 Manual

Preface to AMPAC™ 9 Manual

I. AMPAC™ 9 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. CHN Methods
8. Eigenvector Following
9. Electrostatic Potential
10. Configuration Interaction
11. Polarizability Methods
12. Simulated Annealing
13. COSMO Solvation Model
14. AMSOL Model Module
15. Package Administration
16. References

II. AMPAC™ 9 Examples

17. A Typical Calculation
18. Cartesian Frequencies and Thermodynamics (FORCE)
19. Internal Coordinate Frequencies and Gradients (LTRD)
20. Reaction Pathway
21. Two-Dimensional Grid Search
22. Intrinsic Reaction Coordinate (IRC) Calculation
23. PATH Calculation with Transition Vector
24. Use of Partial Charge Sparkles

III. AMPAC™ 9 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
12.1. Example of a Relatively Rigid System
12.2. Trans-minimum
12.3. Cis-minimum
13.1. Schematic representation of the Solvent Accessible Surface (SAS)
21.1. Inversion of 1,5-hexadiene
24.1. 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 ΔH_f 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
10.1. Possible microstates with 2 CI-active MOs
24.1. Effect of presence of sparkles
A.1. Symmetry Numbers

Copyright © 1992-2009 Semichem, Inc. All rights reserved.


		Contributors