4. Structure and Reactivity

Structure and Reactivity

• 4.1. Geometry Optimizations
  • 4.1.1. Basic Usage
    • 4.1.1.1. Geometry Optimization Thresholds
  • 4.1.2. Initial Hessian for Minimization
  • 4.1.3. Coordinate Systems for Optimizations
    • 4.1.3.1. Redundant Internal Coordinates
    • 4.1.3.2. Coordinate Steps
    • 4.1.3.3. Constrained Optimization
      • 4.1.3.3.1. Running Constrained Optimizations - Examples
    • 4.1.3.4. Constrained Fragments and Molecular Cluster Optimization
  • 4.1.4. Optimization Assuming a Rigid Body
  • 4.1.5. Adding Arbitrary Bias and Wall Potentials
    • 4.1.5.1. Bond Bias Potentials
    • 4.1.5.2. Wall Bias Potentials
  • 4.1.6. Constant External Force - Mechanochemistry
  • 4.1.7. Printing Hessian in Internal Coordinates
  • 4.1.8. Using Model Hessian from Previous Calculations
  • 4.1.9. Geometry Optimizations using the L-BFGS Optimizer
  • 4.1.10. Optimizing with External Methods
  • 4.1.11. Optimization FAQs
    • 4.1.11.1. I can’t locate the transition state (TS) for a reaction expected to feature a low/very low barrier, what should I do?
    • 4.1.11.2. During the geometry optimisation some atoms merge into each other and the optimisation fails. How can this problem be solved?
  • 4.1.12. Some General Notes on Geometry Optimization
  • 4.1.13. Geometry Optimization Keywords
• 4.2. Surface Scans
  • 4.2.1. Theory
  • 4.2.2. Simple Example
  • 4.2.3. Complex Example
  • 4.2.4. Multidimensional Scans
  • 4.2.5. Multiple XYZ File Scans
  • 4.2.6. Surface Scan Keywords
• 4.3. Transition State Searches
  • 4.3.1. Transition State Search Theory
  • 4.3.2. Introduction to Transition State Searches
    • 4.3.2.1. Hessians for Transition State Calculations
    • 4.3.2.2. Special Coordinates for Transition State Optimizations
  • 4.3.3. ScanTS option
  • 4.3.4. Hybrid Hessian
  • 4.3.5. Partial Hessian Vibrational Analysis
  • 4.3.6. Tranistion State Theory Keywords
• 4.4. Intrinsic Reaction Coordinate
  • 4.4.1. Basic Usage
  • 4.4.2. Keywords
• 4.5. Nudged Elastic Band Method
  • 4.5.1. Theory
  • 4.5.2. Spring Forces
  • 4.5.3. Optimization and Convergence of the NEB Method
  • 4.5.4. Climbing Image NEB (CI-NEB)
  • 4.5.5. Generation of the Initial Path
  • 4.5.6. Removal of Translational and Rotational Degrees of Freedom
  • 4.5.7. Optimizations using the Nudged Elastic Band Method
  • 4.5.8. Reparametrization of the Path
  • 4.5.9. Useful Output
  • 4.5.10. Important Warning Messages
  • 4.5.11. Parallel Execution
  • 4.5.12. Zoom-NEB
  • 4.5.13. NEB-TS
  • 4.5.14. FAST-NEB-TS and LOOSE-NEB-TS
  • 4.5.15. NEB / NEB-TS and TD-DFT
  • 4.5.16. Summary of Keywords
• 4.6. Vibrational Frequencies
  • 4.6.1. Mass dependencies
  • 4.6.2. Scaling factors for computed frequencies
  • 4.6.3. Restarting Numerical Frequency calculations
  • 4.6.4. Frequencies keyword list
• 4.7. Thermochemistry
  • 4.7.1. Diagonal Born-Oppenheimer Correction
  • 4.7.2. Spin-Orbit Coupling Correction to the Total Energy
  • 4.7.3. High Accuracy Thermochemistry: the HEAT protocol
• 4.8. Conical Intersections
  • 4.8.1. Gradient Projection
  • 4.8.2. Gradient Projection without NACME
  • 4.8.3. Updated Branching Plane
  • 4.8.4. CI Minima Between Excited States
• 4.9. Minimum Energy Crossing Points (MECP)
  • 4.9.1. Keywords
• 4.10. GOAT: global geometry optimization and ensemble generator
  • 4.10.1. GOAT simple usage example - Histidine
  • 4.10.2. Understanding the output
  • 4.10.3. The final ensemble
  • 4.10.4. GOAT-ENTROPY: expanding ensemble completeness by maximizing entropy
  • 4.10.5. More on the \(\Delta S_{\rm conf}\)
    • 4.10.5.1. Finding rotamers automatically
  • 4.10.6. GOAT-EXPLORE: global minima of atomic clusters or topology-free PES searches
  • 4.10.7. GOAT-REACT: an algorithm for automatic reaction pathway exploration
  • 4.10.8. Exploring geometrical diversity: the GOAT-DIVERSITY option
  • 4.10.9. Automated coarse-grained with GOAT-COARSE
  • 4.10.10. Some general observations
    • 4.10.10.1. Default frozen coordinates during uphill step
    • 4.10.10.2. Parallelization of GOAT
    • 4.10.10.3. Tips and extra details
  • 4.10.11. Keywords
• 4.11. SOLVATOR: Automated Explicit Solvation
  • 4.11.1. Basic Usage
  • 4.11.2. Custom Solvents
  • 4.11.3. Stochastic Method
    • 4.11.3.1. Details on the Stochastic Method
  • 4.11.4. Creating a Droplet
  • 4.11.5. The Wall Potential
  • 4.11.6. Controlling Randomness
  • 4.11.7. Vacuum Search
  • 4.11.8. Keywords
• 4.12. DOCKER: Automated Docking Algorithm
  • 4.12.1. Example 1: A Simple Water Dimer
  • 4.12.2. Example 2: A Uracil Dimer
  • 4.12.3. Example 3: Adding Multiple Copies of a Guest
  • 4.12.4. Example 4: Find the Best Guest
  • 4.12.5. Underlying theory
  • 4.12.6. Looking Deeper into the Output
  • 4.12.7. The final steps
  • 4.12.8. Adding a bond bias to the docking process
  • 4.12.9. Defining the center and extent of the grid
  • 4.12.10. General Tips
  • 4.12.11. Keywords