- •COMPUTATIONAL CHEMISTRY
- •CONTENTS
- •PREFACE
- •1.1 WHAT YOU CAN DO WITH COMPUTATIONAL CHEMISTRY
- •1.2 THE TOOLS OF COMPUTATIONAL CHEMISTRY
- •1.3 PUTTING IT ALL TOGETHER
- •1.4 THE PHILOSOPHY OF COMPUTATIONAL CHEMISTRY
- •1.5 SUMMARY OF CHAPTER 1
- •REFERENCES
- •EASIER QUESTIONS
- •HARDER QUESTIONS
- •2.1 PERSPECTIVE
- •2.2 STATIONARY POINTS
- •2.3 THE BORN–OPPENHEIMER APPROXIMATION
- •2.4 GEOMETRY OPTIMIZATION
- •2.6 SYMMETRY
- •2.7 SUMMARY OF CHAPTER 2
- •REFERENCES
- •EASIER QUESTIONS
- •HARDER QUESTIONS
- •3.1 PERSPECTIVE
- •3.2 THE BASIC PRINCIPLES OF MM
- •3.2.1 Developing a forcefield
- •3.2.2 Parameterizing a forcefield
- •3.2.3 A calculation using our forcefield
- •3.3 EXAMPLES OF THE USE OF MM
- •3.3.2 Geometries and energies of polymers
- •3.3.3 Geometries and energies of transition states
- •3.3.4 MM in organic synthesis
- •3.3.5 Molecular dynamics and Monte Carlo simulations
- •3.4 GEOMETRIES CALCULATED BY MM
- •3.5 FREQUENCIES CALCULATED BY MM
- •3.6 STRENGTHS AND WEAKNESSES OF MM
- •3.6.1 Strengths
- •3.6.2 Weaknesses
- •3.7 SUMMARY OF CHAPTER 3
- •REFERENCES
- •EASIER QUESTIONS
- •HARDER QUESTIONS
- •4.1 PERSPECTIVE
- •4.2.1 The origins of quantum theory: blackbody radiation and the photoelectric effect
- •4.2.2 Radioactivity
- •4.2.3 Relativity
- •4.2.4 The nuclear atom
- •4.2.5 The Bohr atom
- •4.2.6 The wave mechanical atom and the Schrödinger equation
- •4.3.1 Introduction
- •4.3.2 Hybridization
- •4.3.3 Matrices and determinants
- •4.3.4 The simple Hückel method – theory
- •4.3.5 The simple Hückel method – applications
- •4.3.6 Strengths and weaknesses of the SHM
- •4.4.1 Theory
- •4.4.2 An illustration of the EHM: the protonated helium molecule
- •4.4.3 The extended Hückel method – applications
- •4.4.4 Strengths and weaknesses of the EHM
- •4.5 SUMMARY OF CHAPTER 4
- •REFERENCES
- •EASIER QUESTIONS
- •5.1 PERSPECTIVE
- •5.2.1 Preliminaries
- •5.2.2 The Hartree SCF method
- •5.2.3 The HF equations
- •5.2.3.1 Slater determinants
- •5.2.3.2 Calculating the atomic or molecular energy
- •5.2.3.3 The variation theorem (variation principle)
- •5.2.3.4 Minimizing the energy; the HF equations
- •5.2.3.5 The meaning of the HF equations
- •5.2.3.6a Deriving the Roothaan–Hall equations
- •5.3 BASIS SETS
- •5.3.1 Introduction
- •5.3.2 Gaussian functions; basis set preliminaries; direct SCF
- •5.3.3 Types of basis sets and their uses
- •5.4 POST-HF CALCULATIONS: ELECTRON CORRELATION
- •5.4.1 Electron correlation
- •5.4.3 The configuration interaction approach to electron correlation
- •5.5.1 Geometries
- •5.5.2 Energies
- •5.5.2.1 Energies: Preliminaries
- •5.5.2.2 Energies: calculating quantities relevant to thermodynamics and to kinetics
- •5.5.2.2a Thermodynamics; “direct” methods, isodesmic reactions
- •5.5.2.2b Thermodynamics; high-accuracy calculations
- •5.5.2.3 Thermodynamics; calculating heats of formation
- •5.5.2.3a Kinetics; calculating reaction rates
- •5.5.2.3b Energies: concluding remarks
- •5.5.3 Frequencies
- •Dipole moments
- •Charges and bond orders
- •Electrostatic potential
- •Atoms-in-molecules
- •5.5.5 Miscellaneous properties – UV and NMR spectra, ionization energies, and electron affinities
- •5.5.6 Visualization
- •5.6 STRENGTHS AND WEAKNESSES OF AB INITIO CALCULATIONS
- •5.7 SUMMARY OF CHAPTER 5
- •REFERENCES
- •EASIER QUESTIONS
- •HARDER QUESTIONS
- •6.1 PERSPECTIVE
- •6.2 THE BASIC PRINCIPLES OF SCF SE METHODS
- •6.2.1 Preliminaries
- •6.2.2 The Pariser-Parr-Pople (PPP) method
- •6.2.3 The complete neglect of differential overlap (CNDO) method
- •6.2.4 The intermediate neglect of differential overlap (INDO) method
- •6.2.5 The neglect of diatomic differential overlap (NDDO) method
- •6.2.5.2 Heats of formation from SE electronic energies
- •6.2.5.3 MNDO
- •6.2.5.7 Inclusion of d orbitals: MNDO/d and PM3t; explicit electron correlation: MNDOC
- •6.3 APPLICATIONS OF SE METHODS
- •6.3.1 Geometries
- •6.3.2 Energies
- •6.3.2.1 Energies: preliminaries
- •6.3.2.2 Energies: calculating quantities relevant to thermodynamics and kinetics
- •6.3.3 Frequencies
- •6.3.4 Properties arising from electron distribution: dipole moments, charges, bond orders
- •6.3.5 Miscellaneous properties – UV spectra, ionization energies, and electron affinities
- •6.3.6 Visualization
- •6.3.7 Some general remarks
- •6.4 STRENGTHS AND WEAKNESSES OF SE METHODS
- •6.5 SUMMARY OF CHAPTER 6
- •REFERENCES
- •EASIER QUESTIONS
- •HARDER QUESTIONS
- •7.1 PERSPECTIVE
- •7.2 THE BASIC PRINCIPLES OF DENSITY FUNCTIONAL THEORY
- •7.2.1 Preliminaries
- •7.2.2 Forerunners to current DFT methods
- •7.2.3.1 Functionals: The Hohenberg–Kohn theorems
- •7.2.3.2 The Kohn–Sham energy and the KS equations
- •7.2.3.3 Solving the KS equations
- •7.2.3.4a The local density approximation (LDA)
- •7.2.3.4b The local spin density approximation (LSDA)
- •7.2.3.4c Gradient-corrected functionals and hybrid functionals
- •7.3 APPLICATIONS OF DENSITY FUNCTIONAL THEORY
- •7.3.1 Geometries
- •7.3.2 Energies
- •7.3.2.1 Energies: preliminaries
- •7.3.2.2 Energies: calculating quantities relevant to thermodynamics and kinetics
- •7.3.2.2a Thermodynamics
- •7.3.2.2b Kinetics
- •7.3.3 Frequencies
- •7.3.6 Visualization
- •7.4 STRENGTHS AND WEAKNESSES OF DFT
- •7.5 SUMMARY OF CHAPTER 7
- •REFERENCES
- •EASIER QUESTIONS
- •HARDER QUESTIONS
- •8.1 FROM THE LITERATURE
- •8.1.1.1 Oxirene
- •8.1.1.2 Nitrogen pentafluoride
- •8.1.1.3 Pyramidane
- •8.1.1.4 Beyond dinitrogen
- •8.1.2 Mechanisms
- •8.1.2.1 The Diels–Alder reaction
- •8.1.2.2 Abstraction of H from amino acids by the OH radical
- •8.1.3 Concepts
- •8.1.3.1 Resonance vs. inductive effects
- •8.1.3.2 Homoaromaticity
- •8.2 TO THE LITERATURE
- •8.2.1 Books
- •8.2.2 The Worldwide Web
- •8.3 SOFTWARE AND HARDWARE
- •8.3.1 Software
- •8.3.2 Hardware
- •8.3.3 Postscript
- •REFERENCES
- •INDEX
Density Functional Calculations 387
7.2THE BASIC PRINCIPLES OF DENSITY FUNCTIONAL THEORY
7.2.1 Preliminaries
In the Born interpretation (section 4.2.6) the square of a one-electronwavefunctionat any point X is the probability density (with units of for the wavefunction at that point, and is the probability (a pure number) at any moment of finding the electron in an infinitesimal volume dx dy dz around the point (the probability of finding the electron at a mathematical point is zero). For a multielectron wavefunction the relationship between thewavefunction and the electron density is more complicated (involving the summation over all spin states of all electrons of n-fold integrals of the square of the wavefunction), but it can be shown [7] that is related to the component one-electron spatialwavefunctions of a single-determinant wavefunction (recall from section 5.2.3.1 that the Hartree–Fock can be approximated as a Slater determinant of spin orbitals and by
The sum is over n the occupied MOs and for a closed-shell molecule each for a total of 2n electrons. Equation (7.1) applies strictly only to a single-determinant wavefunction but for multideterminant wavefunctions arising from configuration interaction treatments (section 5.4) there are similar equations [8]. A shorthand for
is |
where r is the position vector of the point with |
coordinates (x, y, z). |
|
If the electron density |
rather than the wavefunction could be used to calculate |
molecular geometries, energies, etc., this might be an improvement over the wavefunction approach because, as mentioned above, the electron density in an n -electron molecule is a function of only the three spatial coordinates x, y, z, but the wavefunction is a function of 4n coordinates. Density functional theory seeks to calculate all the properties of atoms and molecules from the electron density. The standard book on DFT is probably still that by Parr and Yang (1989) [9]; more recent developments are included in the book by Koch and Holthausen [10]. The textbook by Levine [11] gives a very good yet compact introduction to DFT, and among the many reviews are those by Friesner et al. [12], Kohn et al. [13], and Parr and Yang [14].
7.2.2 Forerunners to current DFT methods
The idea of calculating atomic and molecular properties from the electron density appears to have arisen from calculations made independently by Enrico Fermi and P. A. M. Dirac in the 1920s on an ideal electron gas, work now well-known as the Fermi–Dirac statistics [15]. In independent work by Fermi [16] and Thomas [17], atoms were modelled as systems with a positive potential (the nucleus) located in a uniform (homogeneous) electron gas. This obviously unrealistic idealization, the
388 Computational Chemistry
Thomas–Fermi model [18], or with embellishments by Dirac, the Thomas–Fermi– Dirac model [18], gave surprisingly good results for atoms, but failed completely for molecules: it predicted all molecules to be unstable toward dissociation into their atoms
(indeed, this is a theorem in Thomas–Fermi theory). |
|
|
The |
(X = exchange, is a parameter in the |
equation; see section 7.2.3.4a) |
method gives much better results [19, 20]. It can be regarded as a more accurate version of the Thomas–Fermi model, and is probably the first chemically useful DFT method. It was introduced in 1951 [21] by Slater, who regarded it [22] as a simplification of the Hartree–Fock (section 5.2.3) approach. The method, which was developed mainly for atoms and solids, has also been used for molecules, but has been replaced by the more accurate Kohn–Sham type (section 7.2.3) DFT methods.
7.2.3 Current DFT methods: the Kohn–Sham approach
7.2.3.1 Functionals: The Hohenberg–Kohn theorems
Nowadays DFT calculations on molecules are based on the Kohn–Sham approach, the stage for which was set by two theorems published by Hohenberg and Kohn in 1964 (proved in Levine [23]). The first Hohenberg–Kohn [24] theorem says that all the properties of a molecule in a ground electronic state are determined by the ground state electron density function In other words, given we can in principle calculate any ground state property, e.g. the energy, we could represent this as
The relationship (7.2) means that is a functional of A function is a rule that transforms a number into another (or the same) number:
A functional is a rule that transforms a function into a number:
The functional transforms the function into the number 4. We designate the fact that the integral is a functional of f (x) by writing
Afunctional is a function of a “definite” (cf. the definite integral above) function. The first Hohenberg–Kohn theorem, then, says that any ground state property of a
molecule is a functional of the ground state electron density function, e.g. for the energy
Density Functional Calculations 389
The theorem is “merely” an existence theorem: it says that a functional F exists, but does not tell us how to find it; this omission is the main problem with DFT. The significance of this theorem is that it assures us that there is a way to calculate molecular properties from the electron density, and that we can infer that approximate functionals will give at least approximate answers.
The second Hohenberg–Kohn theorem [24] is the DFT analogue of the wavefunction variation theorem that we saw in connection with the ab initio method (section 5.2.3.3): it says that any trial electron density function will give an energy higher than (or equal to, if it were exactly the true electron density function) the true ground state energy. In DFT molecular calculations the electronic energy from a trial electron density is the energy of the electrons moving under the potential of the atomic nuclei. This nuclear potential is called the “external potential” and designated and the electronic energy is denoted by (“the functional of the ground state electron density”). The second theorem can thus be stated
where is a trial electronic density and is the true ground state energy, corresponding to the true electronic density The trial density must satisfy the conditions where n is the number of electrons in the molecule (this is analogous to the wavefunction normalization condition; here the number of electrons in all the infinitesimal volumes must sum to the total number in the molecule) and for all r (the number of electrons per unit volume cannot be negative). This theorem assures us that any value of the molecular energy we calculate from the Kohn–Sham equations (below, a set of equations analogous to the Hartree–Fock equations, obtained by minimizing energy with respect to electron density) will be greater than or equal to the true energy (this is actually true only if the functional used were exact; see below). The Hohenberg–Kohn theorems were originally proved only for nondegenerate ground states, but have been shown to be valid for degenerate ground states too [25]. The functional of the inequality (7.6) is the correct, exact energy functional (the prescription for transforming the ground state electron density function into the ground state energy). The exact functional is unknown, so actual DFT calculations use approximate functionals, and are thus not variational: they can give an energy below the true energy. Being variational is a nice characteristic of a method, because it assures us that any energy we calculate is an upper bound to the true energy. However, this is not an essential feature of a method: Møller–Plesset and practical configuration interaction calculations (sections 5.4.2, 5.4.3) are not variational, but this is not regarded as a serious problem.
7.2.3.2 The Kohn–Sham energy and the KS equations
The first Kohn–Sham theorem tells us that it is worth looking for a way to calculate molecular properties from the electron density. The second theorem suggests that a variational approach might yield a way to calculate the energy and electron density (the electron density, in turn, could be used to calculate other properties). Recall that in wavefunction theory, the Hartree–Fock variational approach (section 5.2.3.4) led to the HF equations, which are used to calculate the energy and the wavefunction. An analogous variational approach led (1965) to the KS equations [26], the basis of current
390 Computational Chemistry
molecular DFT calculations. The two basic ideas behind the KS approach to DFT are:
(1) To express the molecular energy as a sum of terms, only one of which, a relatively small term, involves the unknown functional. Thus even moderately large errors in this term will not introduce large errors into the total energy. (2) To use an initial guess of the electron density in the KS equations (analogous to the HF equations) to calculate an initial guess of the KS orbitals (below); this initial guess is then used to refine these orbitals, in a manner similar to that used in the HF SCF method. The final KS orbitals are used to calculate an electron density that in turn is used to calculate the energy.
The Kohn–Sham energy
The strategy here is to regard the energy of our molecule as a deviation from an ideal energy, which latter can be calculated exactly; the relatively small discrepancy contains the unknown functional, whose approximation is our main problem. The ideal energy is that of an ideal system, a fictitious noninteracting reference system, defined as one in which the electrons do not interact and in which the ground state electron density is exactly the same as in our real ground state system: We are talking about the electronic energy of the molecule; the total internal “frozen-nuclei” energy can be found later by adding the internuclear repulsions, and the 0 K total internal energy by further adding the zero-point energy, just as in HF calculations (section 5.2.3.6e).
The ground state electronic energy of our real molecule is the sum of the electron kinetic energies, the nucleus–electron attraction potential energies, and the electron–electron repulsion potential energies (more precisely, the sum of the quantummechanical average values or expectation values, each denoted and each is a functional of the ground-state electron density:
Focussing on the middle term: the nucleus–electron potential energy is the sum over all 2n electrons (as with our treatment of ab initio theory, we will work with a closedshell molecule which perforce has an even number of electrons) of the potential corresponding to attraction of an electron for all the nuclei A:
where is the external potential (explained in section 7.2.3.1, in connection with Eq. (7.6)) for the attraction of electron i to the nuclei. The density function can be introduced into by using the fact [27] that
where is a function of the coordinates of the 2n electrons of a system and is the total wavefunction (the integrations are over spatial and spin coordinates on the left and spatial coordinates on the right). From Eqs (7.8) and (7.9), invoking the concept of
Density Functional Calculations 391
expectation value (chapter 5, section 5.2.3.3) and since we get
So Eq. (7.7) can be written
Unfortunately, this equation for the energy cannot be used as it stands, since we do not know the functionals in and
To utilize Eq. (7.11), Kohn and Sham introduced the idea of a reference system of noninteracting electrons. Let us define the quantity as the deviation of the real kinetic energy from that of the reference system:
Let us next define as the deviation of the real electron–electron repulsion energy from a classical charge-cloud coulomb repulsion energy. This classical electrostatic repulsion energy is the summation of the repulsion energies for pairs of infinitesimal volume elements and (in a nonquantum cloud of negative charge) separated by a distance multiplied by one-half (so that we do not count the repulsion energy and again the energy). The sum of infinitesimals is an integral and so
Actually, the classical charge-cloud repulsion is somewhat inappropriate for electrons in that smearing an electron (a particle) out into a cloud forces it to repel itself, as any two regions of the cloud interact repulsively. This physically incorrect electron self-interaction will be compensated for by a good exchange-correlation functional (below).
Using (7.12) and (7.13), Eq. (7.11) can be written as
The sum of the kinetic energy deviation from the reference system and the electron– electron repulsion energy deviation from the classical system is called the exchangecorrelation energy functional or the exchange-correlation energy, (strictly speaking, the functional is the prescription for obtaining the energy from the electron density function):
The term represents the kinetic correlation energy of the electrons and the term the potential correlation energy and the exchange energy, although exchange and
392 Computational Chemistry
correlation energy in DFT do not have exactly the same significance here as in HF theory [28]; is negative. So using Eq. (7.15), Eq. (7.14) becomes
Let us look at the four terms in the expression for the molecular energy in Eq.(7.16).
1. The first term (the integral of the density times the external potential) is
If we know the integrals to be summed are readily calculated.
2. The second term (the electronic kinetic energy of the noninteracting-electrons reference system) is the expectation value of the sum of the one-electron kinetic energy operators over the ground state multielectron wavefunction of the reference system (Parr and Yang explain this in detail [29]). Using the compact Dirac notation for integrals:
Since these hypothetical electrons are noninteracting can be written exactly (for a closed-shell system) as a single Slater determinant of occupied spin molecular orbitals (section 5.2.3.1; for a real system, the electrons interact and using a single determinant causes errors due to neglect of electron correlation (section 5.4)). Thus, for a four-electron system,
The 16 spin orbitals in this determinant are the KS spin orbitals of the reference system; each is the product of a KS spatial orbital and a spin function Equation (7.18) can be written in terms of the spatial KS orbitals by invoking a set of rules (the Slater– Condon rules [30]) for simplifying integrals involving Slater determinants:
The integrals to be summed are readily calculated. Note that DFT per se does not involve wavefunctions, and the KS approach to DFT uses orbitals only as a way to calculate the noninteracting-system kinetic energy and the electron density function; see below.
Density Functional Calculations 393
3.The third term in Eq. (7.16), the classical electrostatic repulsion energy term, is readily calculated if is known.
4.This leaves us with the exchange-correlation energy functional, (Eq. (7.15)) as the only term for which some method of calculation must be devised.
Devising accurate exchange-correlation functionals for calculating this energy term from the electron density function is the main problem in DFT research. This is discussed in section 7.2.3.4.
Written out more fully, then, Eq. (7.16) is
The term most subject to error is the relatively small term, which contains the (exactly) unknown functional.
The Kohn–Sham equations
The KS equations are obtained by utilizing the variation principle, which the second Hohenberg–Kohn theorem assures us applies to DFT. We use the fact that the electron density of the reference system, which is the same as that of our real system (see the definition at the beginning of the discussion of the KS energy), is given by [7]
where the are the KS spatial orbitals. Substituting the above expression for the orbitals into the energy expression of Eq. (7.21) and varyingwith respect to the subject to the constraint that these remain orthonormal (the spin orbitals of a Slater determinant are orthonormal) leads to the KS equations (the derivation is given by Parr and Yang [31]; the procedure is similar to that used in deriving the Hartree–Fock equations, section 5.2.3.4):
where |
are the KS energy levels (the KS orbitals and energy levels are discussed |
later) and |
(1) is the exchange correlation potential, arbitrarily designated here for |
electron number 1, since the KS equations are a set of one-electron equations (cf. the HF equations) with the subscript i running from 1 to n, over all the 2n electrons in the system. The exchange correlation potential is defined as the functional derivative of with respect to