Molecular Modelling for Beginners

Alan Hinchliffe

• Publisher: Wiley
• Year: 2011
• ISBN:
  9781119964810
• Edition: 1
• Topic: Physical Sciences
• Subtopic: Physical & Theoretical Chemistry

A concise, basic introduction to modelling and computational chemistry which focuses on the essentials, including MM, MC, and MD, along with a chapter devoted to QSAR and Discovery Chemistry.

• Includessupporting website featuring background information, full colour illustrations, questions and answers tied into the text, Visual Basic packages and many realistic examples with solutions
• Takes a hands-on approach, using state of the art software packages G03/W and/or Hyperchem, Gaussian.gjf files and sample outputs.
• Revised with changes in emphasis and presentation to appeal to the modern student.

1

Electric Charges and their Properties

As far as we can tell, there are four fundamental types of interactions between physical objects. There is the weak nuclear interaction that governs the decay of beta particles, and the strong nuclear interaction that is responsible for binding together the particles in a nucleus. The familiar gravitational interaction holds the Earth very firmly in its orbit round the Sun, and finally we know that there is an electromagnetic interaction that is responsible for binding atomic electrons to nuclei and for holding atoms together when they combine to form molecules.

Of the four, the gravitational interaction is the only one we would normally come across in our everyday world. This is because gravitational interactions between bodies always add. The gravitational interaction between two atoms is negligible but when large numbers of fundamental particles such as atoms are aggregated together, the gravitational interaction becomes significant.

You may think it bizarre that there are four types of interaction, yet, conversely, you might wonder why there should be just four. Why not one, three or five? Should there not be a unifying theory to explain why there are four, and whether they are related? As I write, there is no such unifying theory despite tremendous research activity.

1.1 Point Charges

In this chapter I am going to concentrate on electric charges and their properties, since electrons and protons are fundamental building blocks for atoms and molecules.

It turns out that there are two types of electric charge in nature, which we might choose to call type X and type Y (or Red and Blue for that matter, but X and Y will do for now). Experimental evidence shows the existence of an electrostatic force between electric charges; the force between two X-type charges is always repulsive, as is the force between two Y-type charges. The force between an X-type and a Y-type is always attractive. For this reason, the early experimenters decided to classify charges as positive or negative, because a positive quantity times a positive quantity gives a positive quantity, a negative quantity times a negative quantity gives a positive quantity whilst a negative quantity times a positive quantity gives a negative quantity. I am sure you know that the best known fundamental particles responsible for these charges are electrons and protons, and you are probably expecting me to tell you that the electrons are the negatively charged particles whilst protons are positively charged. It is actually just a convention that we take: we could just as well have called electrons positive.

Whilst on the subject, it is fascinating to note that the charge on the electron is exactly equal and opposite of that on a proton. Atoms and molecules generally contain exactly the same number of electrons and protons, and so the net charge on a molecule is almost always zero. Ions certainly exist in solutions of electrolytes, but the number of Na⁺ ions in a solution of sodium chloride is exactly equal to the number of Cl⁻ ions and once again we are rarely aware of any imbalance of charge.

A thunderstorm results when nature separates out positive and negative charges on a macroscopic scale. It is thought that friction between moving masses of air and water vapour detaches electrons from some molecules and attaches them to others. This results in parts of clouds being left with an excess of charge, often with spectacular results. It was investigations into such atmospheric phenomena that gave the first clues about the nature of the electrostatic force.

We normally start any study of charges at rest (electrostatics) by considering the force be...

Table of contents

• Cover
• Title Page
• Copyright
• Preface to the Second Edition
• Preface to the First Edition
• 1: Electric Charges and their Properties
• 2: The Forces between Molecules
• 3: Balls on Springs
• 4: Molecular Mechanics
• 5: The Molecular Potential Energy Surface
• 6: Molecular Mechanics Examples
• 7: Sharing Out the Energy
• 8: Introduction to Statistical Thermodynamics
• 9: Monte Carlo Simulations
• 10: Molecular Dynamics
• 11: Introduction to Quantum Modelling
• 12: Quantum Gases
• 13: One-Electron Atoms
• 14: The Orbital Model
• 15: Simple Molecules
• 16: The HF-LCAO Model
• 17: HF-LCAO Examples
• 18: Semiempirical Models
• 19: Electron Correlation
• 20: Density Functional Theory and the Kohn–Sham LCAO Equations
• 21: Accurate Thermodynamic Properties; the Gn Models
• 22: Transition States
• 23: Dealing with the Solvent
• 24: Hybrid Models; the QM/MM Approach
• Appendix A: A Mathematical Aide-Mémoire
• Appendix B: Glossary
• Appendix C: List of Symbols
• Index