Announcements

We will meet this Friday, September 13, in Room 2109 between 10 am and noon to get an introduction to the Laboratory for Molecular Simulation (LMS). The manager of that facility, Lisa Thomson, will discuss the software available at that facility and give you an introduction to their use. On a separate handout is the homework assignment for this module. You will complete this assignment using the LMS facilities. There are two copies of the text book for this module, Introduction to Computational Chemistry by Frank Jensen, available on 24 hour reserve in the Evans Library. Handouts and lecture slides are available at http://www.chem.tamu.edu/rgroup/lucchese/handouts689/

Reliability of Force Fields

Force fields are usually used to predict to properties: geometries and relative energies. Geometries are relatively easy to obtain and based on the few-body parameters, i.e. stretch, bend, torsion. Relative energies are more difficult to obtain. Relative energies are sensitive to torsional and non-bonded interactions. Small inaccuracies can lead to significant qualitative changes in larger molecules. Example: in cyclododecane, MM2 give 122 conformations and MM3 gives 98 local minima.
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Average Errors of Heats of Formation in MM2

Compound Type Hydrocarbons Ethers and Alcohols Carbonyl compounds Aliphatic amines Aromatic amines Silanes Average Error in Hf (kcal/mol) 0.42 0.50 0.81 0.46 2.90 1.08

Practical Considerations
The input requires:
The type of atoms that are present How the atoms are connected (bonding) A starting guess of the geometry

Thus one cannot discover the bonding in a given system, it is assumed to be known. The input can be provided by numerical input or a graphical interface

Average experimental errors are 0.40 kcal/mol

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Advantages and Limitations of Force Fields

Force fields can be quickly evaluated. This allows the application to modeling biomolecular macromolecules. One can also treat dynamics in these systems. Only feasible method for studying solvent effects or crystal packing. When good parameters are available, good results can be obtained. Force field methods cannot be systematically improved.

Electronic Structure Methods

Slater Determinants The Energy of A Slater Determinant Self-consistent Field Theory Koopmans Theorem The Basis Set Approximation Restricted and Unrestricted Hartree-Fock The Implementation of the SCF Method Semi-Empirical Methods

The Pauli Principle

One of the fundamental postulates of the quantum mechanics of systems with many identical particles (i. e. electrons) is the Pauli Principle. For electrons, the Pauli Principle states that when the coordinates of any two electrons are relabeled, the sign of the wave function must change (antisymmetric): P2,4 (r1, r2 , r3 , r4 ) = (r1, r4 , r3 , r2 ) = (r1, r2 , r3 , r4 ) One way to construct functions with this property is to use determinants. A determinant is a object constructed from a square matrix that yields a single number.
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Determinants
Examples of determinants:

a =a

a b = ad cb c d

a b d e g h

c f = aei + bfg + cdh gec hfa idb i

Swapping rows leads to a change in sign:

c d a b = cb ad = a b c d

Slater Determinants
The wave function of a single electron can be represented by spin orbital: r (1) = (r1 ) (1) where (1) = (1) or (1) The a determinant of such spin orbitals, referred to as a Slater determinant, will yield an antisymmetric wave function: 1 (1) 2 (1) L N (1) 1 1 (2) 2 (2) L N (2) SD (1, 2,K, N ) = L L L N! L 1 ( N ) 2 ( N ) L N ( N )
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Properties of the Slater Determinant

Exchanging electrons thus leads to a swapping of rows in the determinant and a change of sign of the wave function. The determinant also has the property that exchanging any two columns will change its sign. In a Slater determinant, a given spin orbital can only appear once, otherwise two columns would be the same and the value of the determinant would be zero. This property leads to an alternative statement of the Pauli Principle: Two electrons cannot have the same quantum numbers.

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Variational Principle
One can show that in general the electronic wave functions can be written as linear combinations of Slater determinants. Given a guess of the wave function one can estimate the energy using the variational principle:
exact Ee variational Ee

Hartree-Fock Model

trial H e trial trial trial

Approximating the wave function by a single determinant and finding the orbitals that lead to the lowest energy leads to the Hartree-Fock equations.
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The Electronic Hamiltonian

The electronic Hamiltonian can be broken into three types of terms:

Energy Expression
Use an orthonormal set of spin orbitals:

H e = hi + gij + Vnn
i=1 i =1 j>i

N N

0 i j i j = i* (1) j (1)d1 = ij = 1 i = j
Then the denominator of the variational expression is equal to one and the variational energy is then given by: E var = hi +
i=1 N

1 Z hi = i2 2 R ri gij = 1 ri r j

1 ( Jij Kij ) + Vnn 2 i=1 j=1

N N

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Integral Types
The four terms explicitly given in the energy expression are defined as: hi = i (1) h1 i (1) Jij = i (1) j (2) g12 i (1) j (2) K ij = i (1) j (2) g12 j (1)i (2) Vnn =
>

Hartree-Fock Operators
The Hartree-Fock energy can also be written in terms of Coulomb and Exchange operators:
N N 1 E var = i h i + i J j i i K j i 2 j=1 i=1

Coulomb Exchange

+ Vnn

J j i (1) = j (2) g12 j (2) K j i (1) = j (2) g12 i (2)

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Z Z
Rb

i (1)

local operator nonlocal operator

j (1)

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Hartree-Fock Equations
If you vary the orbitals to obtain a minimum variational energy subject to the orthonormality condition, you can show that the spin orbitals must satisfy the Hartree-Fock equations. Fi = ii F = h + (J j K j ) The energies i are known as the orbital energies. These are nonlinear equations and their iterative solution is known as the Self-Consistent Field (SCF) Equations.
j=1 N

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