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Howard A., McIver J., Collins J. (ed.). HyperChem Computational Chemistry

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Howard A., McIver J., Collins J. (ed.). HyperChem Computational Chemistry
HyperChem Computational Chemistry contains two parts. Part 1, the Practical Guide, contains an overview and introduction to the types of calculations that you can perform with HyperChem™. Part 2, Theory and Methods, provides detailed information on the specific implementation of calculations in HyperChem.
This Practical Guide first explores the discipline of computational chemistry and the nature of HyperChem calculations. Next, it examines the concept of a potential energy surface and three calculations of the potential energy surface: single point, geometry optimization, and molecular dynamics. These calculations provide the energies and energy derivatives you need to construct and examine potential energy surfaces. Finally, the Practical Guide illustrates strategies for specific calculations.
Theory and Methods includes the equations, analytical descriptions, and data you need to understand the calculations. It deals with the science behind HyperChem calculations. Information on parameters and settings lets you modify and customize calculations.
Who Should Read this Guide?
Annotated Bibliography
Part I: Practical Guide

Practical Guide Introduction

What is Computational Chemistry?
What is HyperChem?
Building and Displaying Molecules
Optimizing the Structures of Molecules
Investigating the Reactivity of Molecules
Generating and Viewing Orbitals and Electronic Plots
Evaluating Chemical Pathways and Mechanisms
Studying the Dynamic Behavior of Molecules
HyperChem Calculations

Exploring Potential Energy Surfaces
Complexity of Potential Energy Surfaces
Types of Calculations
Single Point
Geometry Optimization
Transition State Search
Molecular Dynamics
Langevin Dynamics
Monte Carlo Simulations
Calculation Methods

Molecular Mechanics
Bonds and Angles
Van der Waals Interactions and Hydrogen Bonding
Electrostatic Potential
United versus All Atom Force Fields
Quantum Mechanics
Molecular Geometry
Calculating Electronic Potential Energy
Range of Quantum Mechanics Methods
Exclusion Principle
Simplified Wave Functions
Hartree-Fock Wave Functions
Extending the Wave Function Calculation
Extending the Wave Function Calculation
Configuration Interaction
Muller-Plesset Perturbation Theory
Molecular Orbitals and Electronic Structure
Orbital Occupancy
Atomic Orbitals and Their Interactions
SCF Technique
Virtual Orbitals
Multiplicity Considerations
Bond Breaking
RHFHalf-Electron Technique
SCF Convergence
Calculation Results
Quantitative Results
Single Point Calculations
Dipole Moment
Total Electron Density
Total Spin Density
Electrostatic Potential
Examples of Single Point Calculations
Geometry Optimizations and Transition State

Geometry Optimizations
Steepest Descent
Conjugate Gradient
Block Diagonal
Eigenvector Following
Setting Convergence Criteria
Examples of Geometry Optimizations
Solvation and Periodic Boundary Conditions
Transition State Searching
Eigenvector Following
Synchronous Transit
Molecular Dynamics

Integration Algorithm
Length of Simulations
Conservation of Energy
Temperature Control
Simulation Periods
Initial Conditions and Heating
Equilibration and Data Collection
Tests for Equilibration
Effect of Solvent on Equilibration
Collecting Data
Examples of Molecular Dynamics Simulations
Constant Temperature versus Constant Energy
Conformational Searching
Quenched Dynamics
Simulated Annealing
Randomization During Molecular Dynamics
Sampling Frequency
When is Conformational Space Adequately Sampled?
Using Geometric Restraints
Using Experimental Data as Restraints
Crossing Energy Barriers
Limiting Conformational Changes during High Temperature Simulations
Docking Molecules
Freezing Part of a System
Solvent Simulations
Choice of Dielectric Constant
Effects on Dynamic Motion
Collecting Averages from Simulations
Evaluating Stability and Equilibration
Constant Energy Simulations
Constant Temperature Simulations
Conformational Searches
Setting Up a Molecular Dynamics Simulation
Heating Time
Simulation or Run Time
Cooling (Annealing) Time
Step Size
Bond Breaking

Langevin Dynamics and Monte Carlo
Langevin Dynamics
Integration Algorithm
Setting Up a Langevin Dynamics Simulation
Heating Time, Run Time, and Cooling Time
Time Step
Constant Temperature vs. Constant Energy
Friction coefficient
Additional Procedures
Monte Carlo Simulations
Background and Method
Monte Carlo Trajectories and Simulation Parameters
Initial Configurations
Step Size and Acceptance Ratio
Initial Phase and Equilibration
Equilibration and Statistical Averaging
Heating and Cooling
Using Molecular Mechanics Methods

Availability of Parameters
Force Field Features
Electrostatic Interactions
Accuracy of Force Fields
Previous Experiences
Choosing Force Field Options
Dielectric Function
1-4 Nonbonded Scale Factors
Nonbonded Cutoffs

Using Quantum Mechanics Methods
Obtaining a Starting Structure
Calculating Part of a Molecular System
Setting Up Options
Selecting Options for the Ab Initio Method
Choosing a Basis Set 1
Add Extra Basis Function
Applying a Basis Set
Charge and Spin Multiplicity
Convergence Criteria
UHF versus RHF
Convergence Acceleration
Calculate Gradient
Calculate MP2 Correlation Energy
Two-Electron Repulsion Integrals
Two-electron Integral Cutoff
Two-electron Integral Buffer Size
Regular Two-Electron Integral Format
Raffenetti Two-Electron Integral Format
Direct SCF Calculation
Initial Guess of MO Coefficients
Number of d Orbitals
Configuration Interaction
Selecting Options for the Extended Hiickel Method
Charge and Spin Multiplicity
Htickel Constant
d Orbitals
Selecting Options for NDO Methods
Convergence Criteria
Charge, Spin, and Excited State
UHF versus RHF
Convergence Acceleration
Configuration Interaction
Log File for Results
Log File for Results
Types of Calculations
Single Point Calculations and CI
Optimization Methods
Transition State Search
Molecular Dynamics
Energy Conservation in Molecular Dynamics Calculations
Contour Plots and Orbitals
Vibrational Spectrum
Electronic Spectrum
Saving Information in a Log File
Extended Htickel Method
Limitations of Extended Huckel
NDO Methods
Defining Electron-Electron Interactions
Treatment of Electron-Electron Interactions
MNDO, AMI, and PM3 Methods
Practical Uses of NDO Methods
Results of Semi-Empirical Calculations
Energies of Molecules
Geometries of Molecules
Energies of Transition States
Molecular Orbital Energies and Ionization Potentials
Dipole Moments
Electrostatic Potential
Atomic Charges
Chemical Reactivity
Atomic Charges and Reactivity
Frontier Molecular Orbitals
Vibrational Analysis and Infrared Spectroscopy
Experimental Characteristic IRFundamental Frequencies
UV-visible Spectra
Choosing a Semi-Empirical Method
Extended Huckel
Further Reading
Part 2: Theory and Methods

Theory and Methods Introduction
HyperChem Architecture
The Back Ends
HyperChem Philosophy
Background on Computational Chemistry
Potential Energy Surfaces
Single Point
Geometry Optimization
Molecular Dynamics
The Born-Oppenheimer Approximation
The Hamiltonian of a Collection of Nuclei and Electrons
The Electronic Hamiltonian
The Nuclear Hamiltonian
Molecular Mechanics versus Quantum Mechanics
Classical Mechanics on a Potential Energy Surface
Force-Energy Generators
Molecular Mechanics
Atom Types
Definition of Atom Type
The Typing Rules
Redefining or Adding Types
Force Fields
Energetic Terms in the Potential
Bond Stretching
Bond Angle Bending
Improper Dihedrals
Van der Waals
Hydrogen Bonding
Effective Dielectric Constants
Terms Involving Vicinal 1-4 Interactions
Bond Stretching
Bond Dipoles
Angle Bending
Bond Stretch and Angle Bending Cross Term
Out-of-Plane Bending
Van der Waals
Bond Stretching
Angle Bending
Improper Dihedrals
Van der Waals
Hydrogen Bonding
Lone Pairs
Van der Waals
Bond Stretching
Angle Bending
Improper Dihedrals
Van der Waals
Hydrogen Bonding
Parameter Sets
Text or DBF Form for Parameters
Modifying Existing Parameter Sets
Creating New Parameter Sets
Compiling Parameters
Chem.ini or Registry Setup of Force Field Options
Periodic Boundary Conditions and Solvent
The Periodic Boundary Conditions
Equilibrated Water Box
Details of Solvation Methodology
Definition of a Restraint
Adding Restraints
The Default MM+ Force Field
The Wild Card Approach
The Default Force Field
Approximate Hybridization
Bond Stretching
Parameters for Butadiene and Related Molecules
Angle Bending
Out-Of-Plane Bends
Single Bonds
Double Bonds
Van der Waals
Quantum Mechanics

Approximate Solutions of the Schrodinger equation
Charge and Multiplicity
Independent Electron Methods
The Independent Electron Approximation
Molecular Orbitals
Orbital Energy Diagrams
The MO-LCAO Approximation
The Matrix equations for the Molecular Orbitals
Solving for the Molecular Orbitals
Self-Consistent Field Methods
Hartree-Fock Method
The Roothaan equations
Spin Pairing
Pople-Nesbet Unrestricted equations
Spin Pairing–Restricted or Unrestricted?
Electronic States
Post Self-Consistent Field Calculations
Configuration Interaction
MP2 Correlation Energy
The Neglect of Differential Overlap Approximation
Characterizations of the Wave function
Contour Plots
Total Electron Density
Spin Density
Orbital Plots
Electrostatic Potential
Mixed Quantum/Classical Model
Choosing the Classical-Quantum Boundary
Capping Atoms and their Parameters
Supported Methods
Ab Initio Method
Normalized Primitive Gaussian Functions
Contracted Gaussian Functions
Minimal Basis Sets: STO-3G
Split-Valence Basis Sets
Polarized Basis Sets
Two-Electron Integrals
Regular Integral Format
Raffenetti Integral Format
Two-Electron Integral Cutoff
Direct SCF Calculation
Initial Guess of MO Coefficients
Projected Huckel
Projected CNDO/INDO
Mixed Model
Extended Huckel Theory
Basic Method
Valence Atomic Orbitals
Hamiltonian Matrix Elements
Choosing a Hiickel Constant
Mixed Model
The CNDO equations
Expectation Values
Mixed Model (CNDO and INDO)
Exchange Phenomena
Differences Between INDO and CNDO
Spin Interactions in INDO
Two-Center Two-Electron Integrals
One-Center One-Electron Integral Hμμ
Two-Center One-Electron Integral Hμν (Resonance Integral)
One-Center Two-Electron Integral
Core-Core Repulsion Integrals
Mixed Model
Two-Center Two-Electron Integrals
One-Center One-Electron Integral Hμμ
Two-Center One-Electron Integral Hμν
One-Center Two-Electron Integrals
Core-Core Repulsion Integrals
Mixed Model (MNDO, AMI, and PM3)
AMI and PM3
Overlap Weighting Factors
Mixed Model
Mixed Model

Computational Options

Single Points on a Potential Energy Surface
Local Minima on a Potential Energy Surface
Unconstrained Geometry Optimization
Optimization Methods
Steepest Descent
Conjugate Gradient Methods
Newton-Raphson Methods
Block Diagonal Newton-Raphson
Transition Structures on a Potential Energy Surface
Transition States Search Methods
Eigenvector Following Method
Synchronous Transit Method
Molecular Dynamics on a Potential Energy Surface
Statistical Averaging
Newton's Equations of Motion
Leap-frog Algorithm
Statistical Mechanical Averages
Random Velocities or Restart Velocities
The Basic Phases of a Trajectory
The Fundamental Time Step
Heating and Cooling
Equilibration at a Temperature T
Collecting Data
Free Dynamics or Constant Temperature Dynamics
Data, Averaging, Snapshot, and Screen Refresh Periods
The Data Collection Period
The Statistical Averaging Period
The Snapshot Collection Period
The Screen Refresh Period
Averaging Energetic and Structural Data
Averaging Energetic Values
Averaging Named Selections
Deviations from the Average
The CSV File
Plotting Instantaneous Values Along the Trajectory
Obtaining and Understanding MD Graphs
Placing Graphs into Other Documents
Collecting Trajectory for Subsequent Playback
Creating a Snapshot (SNP) file
Reading a (HIN, SNP) File for Playback
Global Minima on a Potential Energy Surface
Simulated Annealing
Simple Reactions on a Potential Energy Surface
Trajectory Analysis
Setting Initial Coordinates and Velocities
Temperature Considerations
RHF/UHF Considerations
UV Visible Spectroscopy
Vibrational Analysis and IR Spectroscopy
Vibrational Calculation
Normal Coordinate Analysis
Infrared Absorption
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