0 evaluări0% au considerat acest document util (0 voturi)

381 vizualizări106 paginiJun 21, 2011

© Attribution Non-Commercial (BY-NC)

PDF, TXT sau citiți online pe Scribd

Attribution Non-Commercial (BY-NC)

0 evaluări0% au considerat acest document util (0 voturi)

381 vizualizări106 paginiAttribution Non-Commercial (BY-NC)

Sunteți pe pagina 1din 106

CMBE 598

The user's manual for gaussian is over 200 pages long so a full discussion of the program is well beyond the scope of this document. However, this brief tutorial contains several examples and all the information you need to complete your lab exercise.

A good way to start learning about gaussian is to try a small sample calculation. Create a le containing the lines below. Note that the line numbers in the left column are just for reference and should not be typed. Make sure you leave a blank line at the end of your le.

1 2 3 4 5 6 7 8 9

# HF/STO-3G TEST Water: Single Point Calculation 0 1 O H1 O H2 O

The le you have just created is input deck for gaussian that will compute the energy of a water molecule. Now run gaussian using the le you have created as input. While you are waiting for the run to nish, read the next paragraph which explains what each line in the input deck means. Line 1 is called the route card and always starts with the # sign in the rst column. Gaussian accepts input lines with a maximum of 80 characters, so if your route card is linger than 80 characters you can continue it on subsequent lines (but the # sign is needed only on the rst line). The route card ends with a blank line (line 2 in this case). The format of the route card is always method/basis option1 option2 . . . where the slash (/) is used to separate the method name from the basis set. Multiple options can be used in the same run wih spaces to separate them. A partial list of methods, basis sets, and keywords is given at the end of this 1

document. Since Gaussian output can be very verbose it also recommended to include the tag \T" immediately after the # sign. (That is, replace # with #T.) This switches on \terse" mode, so that less information will be written to the output le. Terse mode will provide more than enough output detail for our purposes. Line 3 is the title card which gives a title and brief description of the job. It can run over one line if necessary. Line 4 terminates the title card. Line 5 gives the total charge and spin multiplicity of the molecule. The spin multiplicity is given by the expression 2 + 1 where is the total spin of the molecule. Note that paired electrons make no contribution to the spin since they have a net spin of zero. Lines 6{8 are called the -matrix. The -matrix gives the positions of the atoms in terms of bond lengths and bond angles. We will say more about the -matrix later.

s s Z Z Z

A guassian ouput le gives considerably more data than we are interested in for this lab. So, rather than trying to explain everything in the output we will focus on the portions that are most useful to us. Each time gaussian completes a self-consistent evaluation of the energy, it prints a report similar to this:

SCF Done: E(RHF) = -74.8272821794 Convg = 0.2631D-03 S**2 = 0.0000

:

This tells us that self-consistency has been achieved and the Hartree-Fock energy of the molecule is ;74 8272821794 atomic units. Since the goal of this calculation was to nd the energy of the molecule, we are done.

3 The Z -matrix

The -matrix is a method of representing atom positions using bond lengths and bond angles. The -matrix for water that we used earlier speci ed that the calculation should contain an oxygen atom, a hydrogen atom located 1.314 A away, and a second hydrogen also 1.314 A away and forming a bond angle with the rst hydrogen of 104.5 degrees. To learn more about the -matrix, let's construct the -matrix for hydrogen peroxide molecule H2 O2 whose structure is shown below

Z Z Z Z

0.9A

105

2

To construct the -matrix, follow these steps: Step 1 Choose an atom to represent the origin. The rst line of the -matrix consists solely of the atom label for this atom. The atom label is the atomic symbol with an optional number to distinguish atoms of the same type. If we choose the left oxygen atom in the illustration then the rst line of the -matrix is:

Z Z Z

O1

Step 2

Chose a second atom bonded to the rst and specify the bond length between the two atoms. The second line of the -matrix is the label for the second atom, the label for the rst atom, and the distance between them (in A). These items may be separated wither by commas or whitespace. If we use the left hydrogen as our second atom the -matrix becomes

Z Z

1 2

O1 H1 O1 0.9

Step 3

Choose a third atom bonded to either of the rst two and specify a bond length and a bond angle. The next line of the -matrix will give the label of the third atom, the label of an atom it is bonded to, the bond length, the label of a third atom, and the bond angle formed by the three. Our only choice in this case for the third atom is the second oxygen, and the -matrix becomes

Z Z

1 2 3

Note that gaussian requires the bond angle to be in the range 0{180 degrees. It also must include a decimal point. Step 4 Chose a fourth atom and specify a bond length, bond angle, and a dihedral angle. The fourth line of our -matrix contains the label for the fourth atom, the label of an atom it is bonded to and the bond length, the label of a third atom and the bond angle formed by the three, and nally, the label of a fourth atom and the value of the dihedral angle formed by the four atom chain. The dihedral angle describes the angle that the fourth atom makes with repect to the plane formed by the other three. It can range either from 0 to 360 degrees or from ;180 to 180 degrees. One way to visualize dihedral angles is called the Newman projection. To form the Newman projection,

Z

imagine the bond between the two middle atoms of the chain is an axis point straight out of the page. Now draw the projections of the other two bonds as if they were the hands of a clock. The angle (measured clockwise from the atom being described) between the hands is the dihedral angle. The Newman projection for hydrogen peroxide is

H1

120

H2

Z

1 2 3 4

For molecules with more than four atoms, Step 4 is repeated until all the atoms are described. Constructing -matrices may seem di cult at rst, especially if you aren't used to thinking about dihedral angles. However with a little practice you will nd it is much easier to translate your estimates for bond lengths and bond angles into a -matrix than it is to do the trigonometry to obtain cartesian coordinates. It is usually a good idea to use a program such as xmol which can read gaussian input decks to visualize molecules and check that your -matrix is correct.

Z Z Z

4 Optimizing Structures

So far we have speci ed all atomic coordinates exactly. This is ne if we want to calculate the energy a particular structure, but it is not very useful if we want to optimize the structure of a molecule. In order to have guassian vary the atomic positions we need to introduce variables into the -matrix that tell gaussian which quantities can be changed. Let's perform a geometry optimization of hydrogen peroxide. Create a le containing the following input deck:

Z

1 2 3 4 5

6 7 8 9 10 11 12 13 14 15

Comparing this input deck to the earlier example, we have changed from the HF method to the MP2 method. We have also added the OPT keyword to the route card to tell gaussian to perform a geometry optimization. Observe that all of the distances and angles in the -matrix for H2 O2 we built earlier have been replaced by variables, and that initial guesses for all the variables have been supplied in a new block that follows the -matrix. Also notice that we have used the variables ROH and A twice to ensure that guassian preserves the symmetry we expect the molecule to have. Run gaussian with this input deck and ROH, ROO, A, and D will be varied until guassian nds the minimum energy structure.

Z Z

In performing a geometry optimization gaussian will perform several single point calculations as it varies the bond lengths and bond angles. Gaussian will print the results of each single point calculation just as in our water example. In this case 11 such calculations are performed as indicated by the lines

Search for a local minimum. Step number 11 out of a maximum of 20

SCF Done: E(RHF) = -148.760433264 Convg = 0.1882D-08 S**2 = 0.0000 A.U. after 8 cycles -V/T = 2.0088

Since we are using the Moller-Plesset correction, the value of the correction is given roughly 10 lines after the HF energy on a line that looks like this:

E2 = -0.8523148579D-01 EUMP2 = -0.14884566475021D+03

E2 is the value of the correction. You can add the correction to the HF energy by hand, or you can look in the archive block at the end of the le. It looks like this: 5

Test job not archived. 1\1\ NATIONAL CENTER FOR SUPERCOMPUTING APPLICATIONS-SIF\FOpt\RMP2-FC\ STO-3G\H2O2\DRICHARD\11-Jul-1997\0\\# MP2/STO-3G TEST OPT\\Hydrogen Pe roxide, Geometry Optimization\\0,1\O,-0.7169492446,-0.052939333,0.0971 278972\H,-0.7596144263,0.4408066747,0.9943698492\O,0.7169430122,0.0529 810408,-0.0971511568\H,0.7596642853,-0.4411403377,-0.9941837728\\Versi on=SGI-G94RevE.2\State=1-A\HF=-148.7604333\MP2=-148.8456648\RMSD=1.882 e-09\RMSF=1.794e-06\Dipole=0.0000282,-0.0001884,0.0001051\PG=C02 X(H2 O2)]\\@

Its not very easy to read, but most of the useful data from the run is in there somewhere. Information about the optimized molecular structure can be found in several places. Several screens after the energy report you will nd a section like this:

Optimization completed. -- Stationary point found. ---------------------------! Optimized Parameters ! ! (Angstroms and Degrees) ! -----------------------------------------------! Name Definition Value Derivative Info. ! ----------------------------------------------------------------------------! R1 R(2,1) 1.025 -DE/DX = 0. ! ! R2 R(3,1) 1.4509 -DE/DX = 0. ! ! R3 R(4,3) 1.025 -DE/DX = 0. ! ! A1 A(2,1,3) 97.0759 -DE/DX = 0. ! ! A2 A(1,3,4) 97.0759 -DE/DX = 0. ! ! D1 D(4,3,1,2) 179.9756 -DE/DX = 0. ! -----------------------------------------------------------------------------

This shows the bond lengths and bond angles for our structure, but its a little di cult to interpret since the variables names aren't the same as the names we used in our input -matrix. A few lines farther on you will nd a distance matrix which gives the distance between all the atoms in the molecule.

Z

1 2 3 4

O H O H

0.000000 1.025011

0.000000

If you scroll a few more lines you will nd the cartesian coordinates of all the atoms.

Standard orientation: ----------------------------------------------------------

Center Atomic Coordinates (Angstroms) Number Number X Y Z ---------------------------------------------------------1 8 0.000000 0.725433 -0.000024 2 1 1.017205 0.851699 0.000193 3 8 0.000000 -0.725433 -0.000024 4 1 -1.017205 -0.851699 0.000193 ----------------------------------------------------------

Finally, in this case guassian has been able to gure out how to express the geometry information in terms of our input -matrix. Just above the archive block we see

Z

Final structure in terms of initial Z-matrix: O H,1,ROH O,1,ROO,2,A H,3,ROH,1,A,2,D,0 Variables: ROH=1.02501149 ROO=1.45086542 A=97.07594599 D=179.9755857

Now we know the optimal structure and energy for hydrogen peroxide.

By default, Gaussian performs a Mulliken population analysis in which the total charge is partitioned among the atoms in the molecule. For example, a Mulliken analysis on a formaldehyde molecule might give:

Total atomic charges: 1 1 C 0.128551 2 O -0.439946 3 H 0.155697 4 H 0.155697 Sum of Mulliken charges=

0.00000

Hence in this case a slight negative charge is placed on the Oxygen atom with compensating positive charge distributed among the remaining atoms. It is important to note that a Mulliken population analysis is not a unique scheme for assiging charge transfer, since it is highly dependent on such factors as the basis set. 7

If the Pop=Full keyword is included in the route section then data about the molecular orbitals will be included in the output le. They are printed at the beginning of the population analysis section, and for formaldehyde appear as:

Molecular Orbital Coefficients 1 2 (A1)--O (A1)--O EIGENVALUES --20.30817 -11.12189 1 C 1S 0.00054 0.99258 2S -0.00720 0.03332 2PX 0.00000 0.00000 2PY 0.00000 0.00000 2PZ -0.00623 0.00071 2 O 1S 0.99429 0.00015 2S 0.02588 -0.00582 2PX 0.00000 0.00000 2PY 0.00000 0.00000 2PZ -0.00558 0.00175 3 H 1S 0.00026 -0.00669 4 H 1S 0.00026 -0.00669 6 7 (A1)--O (B1)--O EIGENVALUES --0.54055 -0.43976 1 C 1S 0.03011 0.00000 2S -0.09915 0.00000 2PX 0.00000 0.61500 2PY 0.00000 0.00000 2PZ -0.45219 0.00000 2 O 1S -0.09207 0.00000 2S 0.49057 0.00000 2PX 0.00000 0.67129 2PY 0.00000 0.00000 2PZ 0.67870 0.00000 3 H 1S 0.16057 0.00000 4 H 1S 0.16057 0.00000 3 (A1)--O -1.33429 -0.12307 0.27967 0.00000 0.00000 0.15641 -0.21890 0.76758 0.00000 0.00000 -0.16894 0.03344 0.03344 8 (B2)--O -0.35599 0.00000 0.00000 0.00000 -0.17238 0.00000 0.00000 0.00000 0.00000 0.88601 0.00000 -0.34277 0.34277 4 (A1)--O -0.80923 -0.18611 0.57459 0.00000 0.00000 -0.22100 0.10157 -0.44161 0.00000 0.00000 -0.16479 0.26576 0.26576 9 (B1)--V 0.28184 0.00000 0.00000 0.81650 0.00000 0.00000 0.00000 0.00000 -0.77089 0.00000 0.00000 0.00000 0.00000 5 (B2)--O -0.64392 0.00000 0.00000 0.00000 0.53463 0.00000 0.00000 0.00000 0.00000 0.41782 0.00000 0.30604 -0.30604 10 (A1)--V 0.63468 -0.20095 1.27622 0.00000 0.00000 -0.51140 0.01904 -0.09973 0.00000 0.00000 0.17097 -0.90840 -0.90840

1 2 3 4 5 6 7 8 9 10 11 12

1 2 3 4 5 6 7 8 9 10 11 12

The atomic orbital contributions for each atom in the molecule are given for each molecular orbital, with the MO's numbered in order of increasing energy|one MO per column. Each MO's energy is listed in the row labeled EIGENVALUES. Just above the eigenvalue row (and below the MO number) is a row giving the symmetry and occupancy (occupied = O, unoccupied = V) of the MO. The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) may be identi ed by nding the point where the occupied/virtual code letter in the symmetry designation changes from O to V. 8

When determining an atomic orbital's contribution to a given MO the most important thing is the relative magnitude of the atomic coe cients (regardless of sign). In the above example, MO 1 has several non-zero coe cients, but the O 1s orbital coe cient is more than an order of magnitude larger than the others. Hence this MO essentially corresponds to the O 1s orbital.

8 Dummy Atoms

Sometimes you will nd that it is di cult to construct a -matrix with the desired properties using only the atoms in the molecule. Consider the case of SiH3. Clearly all three H-Si-H bond angles should be identical. You might consider a -matrix like this:

Z Z

1 2 3 4 5 6 7 8

Z

but this will not enforce the molecular symmetry. In fact, using this -matrix the desired symmetry in only obtained when D and T are related in a special way. We can solve this problem by introducing a dummy atom X which does not interact, but can be used to specify coordinates. In this case we will use a dummy atom as shown in the drawing below. All of the X-Si-H bond angles can be made identical, thus ensuring the desired symmetry. We obtain the -matrix

Z

1 2 3 4 5 6 7 8

The keyword SCAN in the route card instructs gaussian to scan the potential energy over the variables in the the -matrix. For example, you could scan the potenial enegy of a hydrogen dimer using the following input:

Z

1 2

3 4 5 6 7 8 9 10

The last line of the le speci es the scan parameters. In this case R will begin at 0.5 A and scan 10 additional points at 0.2 A invervals. The output of a scan will include all the output for a single point calculation for each scan point and a summary of the energies at the end of the le. For this case the summary is:

Scan Completed. Summary of the potential surface scan: N R HF ---- --------- -----------1 0.5000 -1.04300 2 0.7000 -1.11735 3 0.9000 -1.09191 4 1.1000 -1.03654 5 1.3000 -0.97311 6 1.5000 -0.91087 7 1.7000 -0.85434 8 1.9000 -0.80533 9 2.1000 -0.76418 10 2.3000 -0.73035 11 2.5000 -0.70294 ---- --------- --------------

10 Thermochemistry

Gaussian will compute the vibrational frequencies and other thermochemical data for optimized structures. The easiest way to accomplish this is to use a route card such as

# MP2/3-21G TEST OPT FREQ

which specifes both the OPT and the FREQ keywords. Gaussian will rst optimize the structure and then compute vibrational frequencies using the structure it has just found. Vibrational frequencies can be identi ed in the output by searching for the word Frequencies. The thermochemical data is written in the following form:

Temperature 298.150 Kelvin. Zero-point correction= Pressure 1.00000 Atm. 0.004706 (Hartree/Particle)

10

Thermal correction to Thermal correction to Thermal correction to Sum of electronic and Sum of electronic and Sum of electronic and Sum of electronic and

Energy= Enthalpy= Gibbs Free Energy= zero-point Energies= thermal Energies= thermal Enthalpies= thermal Free Energies=

If we are intereted in calculating the standard heat of reaction then the relevant energy is the one labeled: Sum of electronic and thermal Enthalpies.

11

The following tables give a partial list of methods, basis sets, and keywords known to gaussian. You should nd all that you need for your lab in these tables.

Basis Set Options

Description Minimal basis set: Use for more qualitative results. Double zeta: Two sets of functions in the valence region Adds polarization functions to the heavy atoms. These are six component type functions. 6-31G** Adds polarization functions to hydrogens as well as heavy atoms. 6-31+G* Adds di use functions: Important for systems with lone pairs, anions, excited states. 6-31+G** Adds functions to hydrogens as well. 6-311+G** Triple zeta: Adds extra valence functions (3 sizes of and functions) to 6-31+G**. These are ve pure type functions.

d p s p d

Method Options

Method HF

n

Description Hartree-Fock type calculation. Unless speci ed, RHF is used for singlets, and UHF for higher multiplicites. MP Hartree-Fock calculation followed by an th order MollerPlesset correlation energy correction ( = 2, 3, 4, 5). CIS HF calculation followed by con guation interaction with all single substitutions from the HF reference determinant. CISD HF calculation followed by con guation interaction with all single and double substitutions from the HF reference determinant. QCISD Quadratic CI calculation including sing and double substitutions. QCISD(T) Quadratic CI calculation including sing and double substitutions with triples contribution to the energy added.

n n

12

Keyword Options

Keyword Description FORCE Perform a single analytical calulation of the forces on the nuclei. OPT Perform a geometry optimization over the variables listed in the variables block. FREQ Caclulate force constants, virbational frequencies and other thermochemical data. SCAN Scan the potential surface. TEST Instructs gaussian not to archive the results of the calculation in a central database.

13

Many simulation methods have been developed based on quantum mechanics to predict the molecular nature of molecules and materials. In this course we will focus on: The application of these methods to solving current problems in research How to perform a simulation How to choose a method of simulation How to choose a basis sets, etc. How to understand and interpret our results We will briefly describe the fundamental theory behind these methods. Examples of systems that can be simulated: Reactions: Docking of proteins, enzymes and substrates. Reactions in combustion and atmospheric chemistry Reactions on catalytic metal surfaces. CVD reactions on surfaces for growing thin films. Polymerization reactions Diffusion through a material Properties: Molecular structure, including transition state structure Energy, bond energies, activation energies, heats of reaction Atomic forces Vibrational frequencies, intensities, and transition moments entropy and entropy of reaction Dipole, quadrapole, etc. moments. Electron densities. NMR constants Force constants, Potential energy surfaces, and kinetics

Lecture 1 Page 1

Reactants

Reactor

Products

Reaction Generators

Kinetic Databases

Use Model

No

Model Simplification?

Yes

No

Lecture 1 Page 2

Enthalpy Energy Structure

Zero-Point Energy

Vibrations

Entropy

Structure

Rotations

Vibrations

Barriers

Energy

Zero-Point Energy

Vibrations

Quantum Mechanics Review Lecture 1 Page 3

Examples

Lecture 1 Page 4

Although quantum mechanics has become an extremely useful method for predicting the properties of molecules and materials, it was first developed to explain various effects which could not be explained by classical physics, including: 1) Black body radiation and the ultraviolet catastrophe: Objects do not radiate energy at all frequencies, except at high T. Electromagnetic oscillators are quantized and high energy modes are not active unless enough energy is available. 2) The heat capacity of solids: The heat capacity of solids does not follow the Dulong Petit Law at low temperatures. The atoms of a solid vibrate together as quantized oscillators. High energy vibrations do not contribute to the heat capacity at low T. 3) The photoelectric effect: Electrons are not ejected from a metal, no matter how intense the light if the frequency of the light is below some threshold. The kinetic energy of the ejected electron increases linearly with the frequency of the light, but does not depend on its intensity. Light is composed of particles where the energy is associated with the frequency and the number of particles with the intensity.

Quantum mechanics provided the solutions to the above quandaries by: 1) Quantizing the energies of a system. 2) Combining the wave and particle-like nature of matter. This was done primarily through the development of the wavefunction.

Lecture 2 Page 1

Quantum mechanics is based on four basic postulates: Postulate 1. The state of a system is fully described by the wavefunction.

Postulate 2. Observables are represented by operators which are linear, Hermitian and satisfy the following commutation relations:

[q, p ]= ih

q

[q, q] = 0

[p , p ]= 0

q q

measurement of position along an axis and momentum along that same axis dont commute.

Where q is a position operator (x,y,z) and pq is the corresponding momentum operator. Because the operators are Hermitian they have real eigenvalues and have eigenvectors which form an orthonormal set. Postulate 3. The mean value of the observable O in a series of measurements is equal to the expectation value of the corresponding operator. Measurement of observable O results in one of the eigenvalues of the operator O.

Postulate 4. The probability that a particle will be found in the volume element dx at the point x is proportional to the square of the wavefunction times the volume element dx.

Lecture 2 Page 2

The Wavefunction

The wavefunction plays a critical role in quantum mechanics. It is a mathematical function: whose square gives the probability of finding the particle in a given region of space which contains all the measurable information about a system whose curvature is proportional to the kinetic energy of the particle (the wavelength of the particle is inversely proportional to the kinetic energy) that is the solution to the Schrdinger equation 2

( x)

The probability of finding the particle in the volume d is:

*d

The wavefunction dx

=1

x The bra-ket notation: The expectation value of the observable property O is:

= *d

O = O = *Od

The operator corresponding to the observable O The kinetic energy is proportional to the expectation value of the curvature: Quantum Mechanics Review KE = d2 h2 2M dx 2 Lecture 2 Page 3

Operators

An important aspect of quantum mechanics is its ability to predict properties. This is done by finding a good wavefunction, and then finding expectation value of the property of interest. The following lists some common operators used in quantum mechanics: Position

X=x

p x = ih x

Momentum

Kinetic Energy

h2 2 2 2 h 2 2 2 + 2 + 2= K = 2m x 2m y z

Potential Energy

V = V (x, y, z)

Total Energy

H = K +V

Lx = ih y z z y

L y = i h z x z x

Angular Momentum

Lz = ih x y y x

Lecture 2 Page 4

Superpostion principle

At any given instant a system may be in any eigenstate of a set of eigenstates for a given observable. If it is not in a single eigenstate, it is in a superposition of eigenstates and it is not possible to predict the value of the observable. However, it is possible to predict the expectation value of the observable since it is just the mean of a large number of measurements of that observable since the squares of the amplitudes give the relative probabilities of measuring the possible outcomes of the measurement. Suppose the system is a superposition of states which are eigenstates of the operator :

= cn n

n

n = n n

* * = = cm m cn n d m n

and

* * = cm cn m n d m,n

Since the eigenvectors of form an orthonormal set, the integral above vanishes except when m and n are equal:

= cn cn n n n d = cn cn n = cn n

* * * 2 n n n

Thus the expectation value of the observable is the weighted sum of the probabilities of finding each particular eigenstate times the eigenvalue of that eigenstate (this might remind you of statistical mechanics). Measuring leaves the system in a definite state: that is the act of observation forces the system into an eigenstate of that observable, although which eigenstate we find completely depends on the initial state: the relative weightings of the different eigenstates in initial superposition state.

Quantum Mechanics Review Lecture 2 Page 5

The wavefunction of a system is the one that solves the Schrdinger equation (this can be taken as a postulate of quantum mechanics). The Schrdinger equation is an eigenvalue equation which has the wavefunction as its eigenvector , the Hamiltonian as its operator and the energy as its eigenvalue.

H = E

H =E

For the molecular systems we will consider the Hamiltonian will include the potential energy due to the Coulombic interactions in the molecule:

2 2 2 = V ( x, y , z ) = Z A e + e + Z A Z B e V riA RAB A, B > A i, A i , j > i rij

h 2 i h 2 A Z e2 e2 Z Z e2 A + + A B H = 2m 2 M A i , A riA R AB i i i , j > i rij A, B > A

2 2

Note that the Hamiltonian depends on the wavefunction, and that the wavefunction depends on the Hamiltonian. This makes finding the wavefunction difficult! However, all procedures for finding the wavefunction depend on finding approximate solutions to the Schrdinger equation.

Lecture 2 Page 6

Many-particle wavefunctions

The Pauli Exclusion Principle dictates that up to two electrons can share the same spatial distribution (orbital) and if two electrons are in the same orbital they must have opposite spin.

The above requirement is not automatically satisfied by solutions of the Schrdinger equation because the Hamiltonian does not explicitly depend on spin. However, this requirement can be satisfied by imposing the condition that the wavefunction must be antisymmetric under electron interchange.

So an antisymmetric wavefunction will change sign if the coordinates of any two electrons are exchanged:

( x1 ,..., xr ,..., xs ,..., xn ) = ( x1 ,..., xs ,..., xr ,..., xn )

The requirement that the wavefunction be antisymmetric is called the Antisymmetry Principle and is a general statement of the Pauli Exclusion Principle.

Later we will see that this requirement can be easily imposed by forming wavefunctions in the form of Slater Determinants.

Lecture 2 Page 7

The wavefunction must be antisymmetric with respect to the electronic coordinates, but what about the nuclear coordinates? Since the nuclei are much heavier than the electrons the nuclear kinetic energy is neglected and nucleus-nucleus interactions are considered parametrically:

2 2

Small

Constant

h 2 i Z e2 e2 = A + 2m riA i i, A i , j > i rij

2

H elec

B A

Here the electronic wavefunction is solved for a given set of atomic coordinates. The nuclear coordinates are not explicitly stated in the wavefunction usually.

( x1 , x2 ,..., xn )

Since the nuclei dont move on the same time scale as the electrons (their motions are decoupled), the nuclear wavefunctions look like delta functions on the electronic time scale: = e ( x1 , x2 ,..., xn ) N (A, B,..., N ) = ( x1 , x2 ,..., xn ) (A, B,..., N )

Quantum Mechanics Review Lecture 2 Page 8

For two electrons that have the same spatial quantum numbers, the spatial distribution of probability amplitude is the same and is called an orbital or spatial orbital. Various Atomic Orbitals:

1s 2p 3d

If two electrons occupy the same spatial orbital, they must have different spin. ( x1 , x2 ) = ( x1 , x2 ) ( ) ( )

Spin Orbital

Spatial Orbital

Spin Functions

The spin orbital is the product of the spatial orbital and the spin functions.

= = = =1 =0

Lecture 2 Page 9

Hartree-Products

What form must the wavefunction take for a many-body system? Since the wavefunction is a probability amplitude its square must have the properties of a probability function: If electron 1 and 2 are independent, the probability of finding electron 1 with coordinates x1 and electron 2 with coordinates x2 must equal the product of the independent probabilities of finding electron 1 and electron 2 with coordinates x1 and x2.

P(x 1, x 2 ) = P(x 1 )P(x 2 )

(x 1, x 2 ) = (x1 ) (x 2 )...

( x1 , x2 ) ( x1 , x2 ) = ( x1 ) ( x2 ) ( x1 ) ( x2 )

( x1 , x2 ) ( x1 , x2 ) = ( x1 ) ( x1 ) ( x2 ) ( x2 )

P ( x1 , x2 ) = P ( x1 ) P ( x2 )

Lecture 2 Page 10

Slater Determinants

Although the Hartree Product has the correct form for the probability density, it is not antisymmetric:

1 ( x1 ) 2 ( x2 ) 1 ( x2 ) 2 ( x1 )

The Slater determinant is a way of ensuring both the antisymmetry of the wavefunction, as well as the correct form of the probability:

1 ( x1 ) 2 ( x1 ) ( x ) 2 ( x2 ) (1,2,..., n ) = 1 2 M M 1 ( xn ) 2 ( xn )

K n ( x1 ) K n ( x2 ) O M L n ( xn )

If any two rows are exchanged, the wavefunction changes sign: The wavefunction is antisymmetric. The form of the wavefunction is a sum of Hartree-products, each with a sign depending on whether the permutation is even or odd. This also allows for correctly treating the indistinguishability of the electrons. (Each electron finds itself in every orbital with equal weight).

Lecture 2 Page 11

Since according to the variational principle the expectation value of H for any approximate wavefunction is always larger than that of the exact ground state:

H E0

A method for detemining wavefunctions can be developed which uses the expectation value of H as measure of the quality of the wavefunction: That is we want to minimize the quantity:

H = t H t

If we expand the trial wavefunction in a set of basis functions then we have variational parameters: the coefficients of the basis functions.

trial = ci i

i

H =

c

i i

c

i i

When we proved the variational principle we used a basis of the eigenfunctions of H. Here we cannot do that because the wavefunction is the unknown. In fact, we dont even know the Hamiltonian:

Z e2 e2 h 2 i A + H = 2m riA i i, A i , j > i rij

2

B

Electron-Electron interaction depends on the wavefunction

A

Lecture 4 Page 1

Although we can use the variational principle to solve the Schrodinger equation, the method of solution is not obvious because the wavefunction depends on the Hamiltonian, and the Hamiltonian depends on the wavefunction:

H( )

H ( ) ( H ) = E ( ) ( H )

Hartree and Fock independently developed a method to overcome this difficulty: 1: Guess a trial wavefunction (this amounts to guessing the basis coefficients) 2: Calculate the expectation value of F for this trial wavefunction where F is an operator which replaces the electron-electron Coulomb interaction with the interaction of each electron with the average field of the other electrons. 3: Minimize the expectation value of F with respect to the expansion coefficients 4: Take the new wavefunction from step 3 and repeat steps 2 and 3 until he new wavefunction obtained is equal to the one from the previous iteration. So instead of solving the Schrodinger equation we solve the Hartree-Fock equations:

F (i ) (i ) = (i )

Z F = i A + HF (i ) 2 i i , A riA

2

Lecture 4 Page 2

Because HF is an interative procedure which ends when self-consistency is reached (according to some threshold criteria) it is called a Self-Consistent Field theory. The word field signifies the property that electrons only interact in an average way: they move in the average field of the other electrons. HF does not contain dynamic correlation: That is the only correlation in HF is that due to the average field, and that due to exchange correlation between like spins. The improvements more accurate methods based on HF make are due to including dynamic correlation: usually just called correlation. HF is one of the most efficient ab initio methods: Its characteristics are: It overestimates vibrational frequencies by about 10 percent. It produces very accurate geometries Transition states energies are usually overestimated (50-300 percent) Bond energies are underestimated. HF is a good base theory, and often used for initial exploration of the properties of a system.

Lecture 4 Page 3

For the doubly occupied orbital:

(1,2) = 1s1s 1s 1s 1s1s 1s 1s

2

2

(1,2) = 1s 1s 1s 1s 1s 1s 1s 1s 1s 1s 1s 1s + 1s 1s 1s 1s

Note that the cross terms vanish due to the orthogonality of the spin functions:

(1,2 ) = 1s 1s

2 1

Also note that this wavefunction was not normalized: When making Hartree-product, or Slater determinant wavefunctions we add a normalization factor:

1 ( x1 ) 2 ( x1 ) 1 1 ( x2 ) 2 ( x2 ) (1,2,..., n ) = M n M 1 ( xn ) 2 ( xn )

K n ( x1 ) K n ( x2 ) O M L n ( xn )

1s 1s

+ 1s 1s 2

1s 1s

Quantum Chemistry Basics

Lecture 4 Page 4

For the doubly occupied orbital:

(1,2 ) = 1s 2 s 2 s1s 1s 2 s 2 s1s

2

2

(1,2) = 1s 1s 2 s 2 s 1s 2 s 2 s 1s 2 s 1s 1s 2 s + 2 s 2 s 1s 1s

(1,2 ) = 1s 1s 2 s 2 s 1s 2 s 2 s 1s 2 s 1s 1s 2 s + 2 s 2 s 1s 1s

2

The cross-term does not vanish: There is Correlation between the motions of electrons with the same spin: This is called Exchange Correlation. Hartree Fock contains this Correlation automatically.

Lecture 4 Page 5

Basis Functions

There are many choices in making an expansion of atomic-like wavefunctions in a set of basis functions:

=

c

i =1 i

We can include basis functions with the same nodal behavior as the atom: that is with the same angular momentum quantum numbers: H: 1s functions C: 1s, 2s and 2p functions Si: 1s, 2s, 2p, 3s, and 3p functions To improve the description of bonds we often include polarization functions: this improves the ability of the basis set to describe distortion of electrons. We might add: H: 2p functions (and even 3d functions if very high accuracy is desired) C: 3d functions (and even 4f functions) Si: 3d functions (and even 4f functions), etc.

Lecture 4 Page 6

Basis Functions

Diffuse functions can also be added: These functions have the same angular momentum quantum number as the valence shell, but are even more diffuse than those included in double zeta, and triple zeta basis sets: Double zeta refers to the number of different exponents used to describe a valence orbital. Thus, double zeta means using tight and diffuse functions. Triple zeta means using tight, medium and loose functions. Slater-like (STO)

i

c

i =1 i

i = exp( r )

i = exp( r

Gaussian

Gaussian functions are generally used because integrals of Gaussian functions, and products of Gaussian functions are simpler than integrals of Slater functions. However, this introduces an error because the Cusp at r=0 is not sharp for a Gaussian function unless zeta goes to infinity: To overcome this Contractions are used: A contraction is a fixed sum of Gaussian functions of varying zeta which approximate the Slater form and together are taken as a single basis function: This is especially important for core orbitals, but is often included for tight valence orbitals as well:

i = g j j

j =1

Lecture 4 Page 7

Basis Sets

3-21G 6-31G 3-21G(d) One triply contracted core function, one doubly contracted tight valence function, a loose valence function One six-fold contracted core function, one triply contracted tight valence function, a loose valence function One triply contracted core function, one doubly contracted tight valence function, a loose valence function One set of d polarization functions on heavy atoms 6-31G(d) One six-fold contracted core function, one triply contracted tight valence function, a loose valence function One set of d polarization functions on heavy atoms 6-31G(d,p) One six-fold contracted core function, one triply contracted tight valence function, a loose valence function One set of d polarization functions on heavy atoms, a set of p polarization functions on H 6-311G(d) One six-fold contracted core function, one triply contracted tight valence function, one medium and one loose valence function. One set of d polarization functions on heavy atoms 6-311G(d,p) One six-fold contracted core function, one triply contracted tight valence function, one medium and one loose valence function. One set of d polarization functions on heavy atoms, and a set of p polarization on H. 6-311G(2df,p) One six-fold contracted core function, one triply contracted tight valence function, one medium and one loose valence function. A tight and loose set of d polarization functions on heavy atoms, a set of p polarization functions on H. 6-311+G 6-311G plus a set of diffuse valence functions on heavy atoms 6-311++G 6-311G plus a set of diffuse valence functions on heavy atoms, and H. 6-311++G(3df,pd)

Lecture 4 Page 8

Basis Sets

Triple Valence 3-fold tight Valence Contraction 3 d Sets and an F Set of Polarization on Heavy Atoms

6-311++G(3df,pd)

6-fold Contracted Core Diffuse Functions on Heavy and Light Atoms p Set and an d Set of Polarization on H

6-31+G(2d, p)

6-fold Contracted Core

Quantum Chemistry HF Basics

p Set of Polarization on H

Lecture 5 Page 1

The variational principle states that the expectation value of H for any approximate wavefunction is always larger than that of the exact ground state:

H E0

Consider a trial wavefunction expanded in a basis of eigenfunctions of H We can write: Substitute in our expansion:

trial = cii

i

H E0 = t H i E0 t H E0 =

c

i i

H E0

c

i i

H E0 =

c

i i i

E i E0

c

i i

Remove constants from the integral: Include the orthogonality and sign of the integral:

H E0 = c*i ci (E i E0 ) i i H E0 = c*i ci (E i E0 ) 0

i

Lecture 5 Page 2

Rayleigh-Ritz Method

The Rayleigh-Ritz Method uses a linear combination of fixed basis functions to apply the variational principle.

trial = cii

i

H = H = t i t t t

= H =

c

i i i i

c

j j j j j

c c

i

c c

i i, j i i, j

i H j

j

c c

i j

c c H = c c S

i j i, j i j i, j

ij

ij

H ij Sij = 0

Lecture 5 Page 3

The spinorbitals that give the lowest energy for a single determinant wavefunction are found using the variational Method. The Hartree-Fock approach involves replacing the full Hamiltonian with a sum of one electron Hamiltonians where each electron interacts with the average field of the other electrons. N Fock equations:

f1 (i ) = (i )

Z f1 = i A + HF (1) 2 A rA 1

2

Z F = i A + HF (i ) 2 i i , A riA

2

u

Coulomb Operator:

a (1) u (1)

Exchange Operator:

Lecture 5 Page 4

Hartree-Fock Method

Calculate F no

Convergence

yes

Lecture 5 Page 5

Configuration Interaction

The HF wavefunction is the lowest energy single determinant solution to the Schrodinger equation: Other wavefunctions based on HF can be written which have multiple determinants (configurations):

CI

= HF + cs s + cd d + ct t

s d t

1 ( x1 ) r ( x1 ) ( x ) r ( x2 ) r = 1 2 M M 1 ( xn ) r ( xn )

K n ( x1 ) K n ( x2 ) O M L n ( xn )

A doubly excited determinant would have two HF spin orbitals replaced by virtual orbitals

Lecture 5 Page 6

Contraction Examples

Spatial parts of spin orbitals are expanded over a set of basis functions:

=

cusp

cii

i =1

i = g j j

j =1

r

i = g j j

j =1 m

Since the actual spin orbitals are slater like, contractions of Gaussian functions are used to approximate the cusp of a Slater Type Orbital.

3-21G 2 9 13 6-31G 2 9 13 6-31G(d) 2 14 18 6-31G(d,p) 5 14 18

r

H 1st Row 2nd Row 6-311G(d,p) 6 18 22 6-311+G(d,p) 6 22 26 6-311+G(2df) 3 37 41 6-311++G(2df,p) 7 37 41

6-31G(d)

6-311+(d,p)

H C Si H C Si

2s 0 2 1(6) 0 4 1(6)

2p 0 6 3(6) 3 12 3(6)

3s 0 0 2 0 0 4

3p 0 0 6 0 0 12

3d 0 5 5 0 5 5

Lecture 6 Page 1

Single Excitations

The HF wavefunction is the lowest energy single determinant solution to the Schrodinger equation. Using the HF wavefunction as a reference we form singly excited determinants by replacing each orbital by a virtual orbital. One HF spin orbital replaced by a HF virtual orbital

1 ( x1 ) 1 ( x2 ) = 1 ( x3 ) M 1 ( xn )

K a ( x1 ) K n ( x1 ) K a ( x2 ) K n ( x2 ) K a ( x3 ) K n ( x3 ) M M O M K a ( xn ) K n ( xn )

1 ( x1 ) 1 ( x2 ) r a = 1 ( x3 ) M 1 ( xn )

K r ( x1 ) K n ( x1 ) K r ( x2 ) K n ( x2 ) K r ( x3 ) K n ( x3 ) M M O M K r ( xn ) K n ( xn )

Brillouins Theorem: Singly excited determinants do not directly mix with the ground state.

CIS

= HF + cs s = HF

s

CIS

r r r H CIS = HF H HF + cs HF H a + cs cs a H a = HF H HF

Lecture 6 Page 2

Using the HF wavefunction as a reference we form doubly excited determinants by replacing two orbitals by two virtual orbitals.

rs ab

1 ( x1 ) 1 ( x2 ) = 1 ( x3 ) M 1 ( xn )

K r ( x1 ) K s ( x1 )K n ( x1 ) K r ( x2 ) Ks ( x2 )K n ( x2 ) K r ( x3 ) Ks ( x3 )K n ( x3 ) M M O M K r ( xn ) Ks ( xn )K n ( xn )

Singles

Doubles Triples

HF

The HF ground state can directly mix with doubly excited determinants: Thus, because of Brillouins theorem we expect that double excitations will be the leading corrections to the HF wavefunction.

CID

rs = HF + cd ab d

CID

rs rs rs H CID = HF H HF + cd HF H ab + cd cd ab H ab

Higher and higher order configurations can be used to improve the wavefunction, however the corrections get smaller and the expense of the calculation grows geometrically.

Lecture 6 Page 3

CI

Choose Structure, Spin and Charge

HF Loop

Calculate F no Calculate Energies and New coefficients Convergence

Lecture 6 Page 4

Multi Reference CI

In addition to expanding the wavefunction based on configurations made from exciting out of a HF reference, we can also use multiple reference states in the CI expansion. This might be done if certain electronic configurations are expected to be important:

S d S d = HF + cs HF + cd HF + ... + cs ref + cd ref + ... S D S D

MRCI

The reference states are often chosen as low lying excited states which have replace orbitals that are active in the process being considered (say a chemical reaction).

HF

Lecture 6 Page 5

MCSCF

Choose Structure, Spin and Charge

HF Loop

Calculate F no Calculate Energies and New coefficients Convergence

MCSCF Loop

Hold CI expansion fixed and reoptimize orbitals

Lecture 6 Page 6

Multiconfiguration SCF

MCSCF involves first doing a CI calculation using the fixed spin orbitals (usually from HF) to determine the CI expansion coefficients, then reoptimizing the orbitals and repeating the process iteratively until selfconsistency is reached.

Doubles

MRCI

S d = HF + cs HF + cd HF + ... S D

Singles

Triples

HF

This process thus involves an inner and outer iterative process to obtain the best wavefunction. NOTE: MCSCF wavefunctions are extremely expensive to calculate! Many scale as N6. Examples of MCSCF methods include: CASSCF, and GVB*CI.

Lecture 6 Page 7

Symmetry

Molecular symmetry can be used to reduce the cost of an electronic structure calculation: Linear combinations of atomic orbitals can be constructed which are representations of the overall molecular symmetry. These are called symmetry adapted linear combinations of AO. Molecular orbitals can be formed by combining these linear combinations of atomic orbitals. The symmetry of the underlying SALC imposes relationships between the two electron integrals between electrons. These relationships can be used to determine integrals without calculating them.

QC Practical Issues

Lecture 7 Page 1

Combining atomic orbitals of atoms that are related by symmetry:

0 Nodes

1 Node

2 Nodes

3 Nodes

QC Practical Issues

Lecture 7 Page 2

We can make combinations of SALC of atomic orbitals to form molecular orbitals:

+ +/+ +

QC Practical Issues

+

Lecture 7 Page 3

Symmetry

Note: Not all symmetry can be used by QC methods (only abelian groups can be used). If mirror planes and Cn axis exist in your system, input molecules such that this symmetry exists and can be recognized by the program. Use geometry variables that are the same for distances, angles etc. that are related by symmetry. Use high symmetry planes, axis to define your molecule. Speed improvements are approximately a factor of 2 for each used mirror plane. Interpretation of nodal planes, molecular orbitals etc. will be easier if symmetry is used.

C2

C3

In order for program to use mirror plane, dihedral angle must be 180 degrees and symmetry related bonds and angles must be input equally.

QC Practical Issues

Lecture 7 Page 4

Bond Energy

Bond energy is the difference between the energy of a molecule and two fragments of the molecule made by separating an atom from the rest of the molecule. This can be done by calculating the fragments separately, or together (spaced far apart). Because of scaling not being linear, better to calculate separately (usually). If the molecule is not allowed to relax, then the bond energy is called a snap bond energy.

QC Practical Issues

Lecture 7 Page 5

When inputting a QC calculation the charge state of the molecule must be specified. The charge state must be an integer. Specifying charge states other than zero allows the calculation of ions. To calculate the electron affinity of a molecule calculate the energy difference between the molecule and the anion state (charge state -1) To calculate an ionization potential, calculate the energy difference between a molecule and its cation state (charge state +1). Second and third ionization potentials can be calculated in a similar fashion.

The spin state of the molecule must also be specified when inputting an electronic structure calculation. For closed shell systems, the spin state is a singlet (s=0) For a system with a single dangling bond, the charge state is usually a doublet (s=1/2) For a system with multiple unpaired electrons, the charge state is not often obvious.

QC Practical Issues

Lecture 7 Page 6

Ethylene example

Ethylene: Closed shell (singlet), neutral molecule. 4 CH bonds, a C-C sigma bond, and a C-C pi bond. CH ~ 1.09, CC ~ 1.31 . 3 mirror planes. To calculate EA: change charge state to -1 and spin state to 1. Recalculate energy (opt?) Energy To calculate IP: change charge state to +1 and spin state to 1. Recalculate energy (opt?) C-C sigma antibond LUMO HOMO C-C pi antibond C-C pi bond C-C sigma bond C-H bonds HOMO: The highest occupied molecular orbital. LUMO: The lowest unoccupied molecular orbital. C 1s Core Calculating triplet state involves changing spin state to 2 (opt?). An electron is promoted to the pi antibond.

QC Practical Issues

Lecture 7 Page 7

Methylene example

Methylene: Neutral molecule. Singlet or triplet? 2 CH bonds CH ~ 1.09 2 mirror planes. (C2V symmetry, like water).

Energy

Energy

C 1s Core

C 1s Core

QC Practical Issues

Lecture 7 Page 8

Ethylene example

Ethylene: Closed shell (singlet), neutral molecule. 4 CH bonds, a C-C sigma bond, and a C-C pi bond. Enthylene dissociates into two triplet CH2 methylenes. To calculate the dissociation energy the fragments must be in their triplet state.A better dissociation energy would be found by allowing the CH2 groups to relax. The rotational barrier is overestimated if the molecule is not allowed to relax. This is because the CC distance is too short for a sigma bond. The molecule compromises in the case where it can form a pi bond, but when the pi bond is broken the molecule will relax to its equilibrium C-C single bond distance (about 1.5). E RCC E RCC

Lecture 8 Page 1

Methylene example

sp2

sp2

In order to improve the bonds, C increases the S character leaving a dangling bond a pure p state. Since it costs energy to (hybridize) increase the p character a lower energy can be obtained in the sp2 state. Also note that for C less p character increases the HCH angles moving the Hs further apart from each other. For silicon the p orbitals are relatively small and the hybridization energy is low as well. It thus takes more p character to make a good bond and little penalty must be paid in order to hybridize.

Lecture 8 Page 2

Correlation Energy

The correlation energy of a molecule is defined as the difference between the exact energy and the HF energy. HF doesnt allow electrons to instantaneously interact and thus dynamic correlation is not included. In order to describe many effects it is crucial to include dynamic correlation. Thus many methods have been developed in order to improve upon the HF wave function (CI methods, for example).

g = l +r

u = l r

= g + u

= g u

Using the antibond configuration in a CI expansion allows the electronic wavefunction to correlate the electron motion between the left and right H atoms. This becomes more important as the molecule dissociates.

Lecture 8 Page 3

The most important kind of correlation for describing bonding and transition states is left-right correlation. Bonds The next most important type of correlation is angular correlation. To describe angular correlation it is important to include polarization functions in the basis set expansion. Lone pair electrons. In-out correlation is radial correlation. Here an electron near a nucleus will cause other electrons to prefer larger distances from that nucleus. Hartree-Fock underestimates bond strengths because it does not include dynamic electron correlation. When a molecule dissociates the electrons are found on their respective nuclei: there is nearly complete correlation between the electron motion. HF on the other hand forces the electrons to both be in the vicinity of one nucleus with independent probabilities, even when there is infinite separation between the nuclei. The energy of the dissociated state is severely overestimated.

g = l +r g = l +r

Lecture 8 Page 4

Geometry Optimizations

One of the primary goals of QC is to predict atomic structures, including transition states. In many cases the structure itself is the quantity of interest. In all cases the energy depends on the structure so obtaining good energies means using good structures. Examples of this include the improvements that can be made from snap bonds energies, rotational barriers, and other energies when the molecule is allowed to relax during a distortion. Question: How do you predict new structures? Short answer: Use the optimization (opt) or transition state (TS) keywords in Gaussian Question: What is Gaussian doing? Answer: It uses the Hellmann-Feynman Theorem to calculated forces.

dH dE = dP dP

The derivative of the energy with respect to some parameter is the expectation value of the derivative of the Hamiltonian with respect to that parameter. Since forces are derivatives of energy with respect to moving a nucleus we must determine derivatives of H with respect to the nuclear coordinates.

Lecture 8 Page 5

Geometry Optimizations

Once the wave function is obtained for a given structure, forces at that geometry are obtained by taking the expectation values of the derivatives of the Hamiltonian for that wave function:

dH dE dH = = dRA dRA dRA

Once the forces are obtained, the atoms are allowed to move according to the forces, the masses of the atoms and a quasi-time that the forces are allowed to act. Gaussian chooses the step size, but it can be changed. The nuclei thus move in the potential described by the energy as a function of geometry. Once the new structure is obtained the wave function has to be calculated at that structure: the derivatives evaluated and new forces calculated. These forces are allowed to act to produce a new structure and the process repeats until: small RMS forces are obtained. No one force exceeds some maximum value small RMS displacements are obtained. No one displacement exceeds some maximum value.

Lecture 8 Page 6

Optimizations

Although structure prediction can be very accurate, several key points should be kept in mind when using Gaussian to predict new structures: Use as good of a guess for a structure as you can: You can save enormous amounts of CPU time. Structures are not generally very sensitive to basis sets: you can use a more approximate basis set to do the first rough optimization and refine the optimization later with a bigger basis. HF generally predicts structure quite accurately. If you have no idea what structure to use, find molecules with analogous fragments/groups and use those structural parameters as starting guesses. Be careful not to allow symmetry to be too high: Too much symmetry will cause some forces to be zero: example: planar ammonia. If you dont know your molecule/system well and the system is quite large, optimizations of fragments of the molecule can help for starting points for determining the structure of the whole system. If atoms are equivalent, use equivalent parameters to describe the atomic positions which will reduce the number of degrees of freedom and speed up the calculation. For difficult cases force constants can be used (the book describes these options on pages 47-48)

Lecture 8 Page 7

Optimizations

Be aware that an optimization will tend to find the nearest local minimum of the energy surface. Thus, the predicted geometry may not be the correct one: again, the starting guess is important. It may also be necessary to check different conformers, etc. Optimizations are much slower than single point calculations: Expect calculations to take longer!

Lecture 8 Page 8

Transition States

Transition state: often, as a molecular system undergoes a chemical transformation it must go over an activation barrier. The energy is the energy of a saddle point on the potential energy surface for the chemical reaction. This usually occurs because a system must first partially break existing bonds in order to form new bonds. Example: H2 + H As an H atom approaches H2 molecule, the good overlap with the closest H atom in H2 is not enough to make up for the perturbation this electron has on the original H2 bond. (they must be orthogonal to each other). 0 Nodes SALC I must put 3 electrons into the three orbitals at the left. Two in the lowest energy orbital and one in the second lowest energy orbital (which is nonbonding). E RHH

1 Node SALC

2 Nodes SALC

QC Optimizations and Correlation Lecture 8 Page 1

Transition States

Gaussian can optimize for transition states by minimizing the forces on the molecule with the restriction that the molecule have one negative frequency (the molecule is at a saddle point). Notes: Transition state searches are sometimes difficult because the wave function is harder to describe at the TS. The transition state geometry is harder to guess. Often times we guess structures where the active bonds are stretched 15 to 20 percent. TS are usually very sensitive to basis sets, and level of theory. To optimize to a TS use one of the TS keywords: Some key words use interpolation between reactants and products to guess structures. Other methods use PES curvature information from frequency calculations. It is often best to search for transition states with a lower level of theory and lower basis set to get a good approximation to what the TS should look like.

Lecture 8 Page 2

Frequency Calculations

The Helmann Feynman theorem allows us to calculate forces and frequencies. The second derivative matrix is known as the Hessian:

2 2 2 d H d E d H = = dRAdRB dRA dRB dRAdRB

The eigenvalues of this matrix are proportional to the frequencies squared (using the Harmonic approximation, and dividing by the reduced mass of the vibrational mode). E

=

k m

Normal modes are the eigenvectors of the Hessian and describe the relative displacement vectors on each atom for the different vibrational modes. Gaussian calculates vibrational frequencies for a given molecule at a particular structure, level of theory, etc. These calculations scale one order greater than energy calculations.

Lecture 8 Page 3

Frequency Calculations

Frequencies often are systematically high for a given level of theory and can thus be systematically corrected. This is usually done with a multiplicative scaling factor. For HF the scaling factor is about 0.89. The best estimate for the vibrational frequencies using a HF frequency calculation is 0.89 times the HF frequencies. Each level of theory will have its own scaling factor. The scaling factor can be determined by calculating the frequencies for a molecule where the frequencies have been accurately measured and assigned. Often, certain modes, such as inversion and dihedral torsion will not scale and these modes are often not corrected.

Lecture 8 Page 4

Frequencies

Frequencies can be used for several different things: 1) They can be used to identify molecular species 2) Help make assignments 3) Determine the zero point energy and make ZPE corrections to energies 4) Determine vibrational partition functions to determine vibrational entropy and pre exponential factors. 5) Characterizing stationary points. 6) Obtaining force constants to aid in TS searches.

ZPE

Lecture 8 Page 5

Levels of Theory

Gaussian can perform many different types of calculations. Well not go into all of these, but we will describe several of them during the course. We list them know so that you will be aware of them to use them as you wish: HF (UHF, RHF) MP2 MP4 CIS CISD CISD(T) CASSCF QCISD QCISD(T) CCSD CCSD(T) G2 BLYP B3LYP B3PW91

Lecture 8 Page 6

Levels of Theory

Gaussian can perform many different types of calculations. Well not go into all of these, but we will describe several of them during the course. We list them know so that you will be aware of them to use them as you wish: HF (UHF, RHF) MP2 MP4 CIS CISD CISD(T) CASSCF QCISD QCISD(T) CCSD CCSD(T) G2 BLYP B3LYP B3PW91

Lecture 8 Page 1

Configuration Interaction (CI) methods allowed us to systematically correct the Hartree-Fock wave function by mixing in higher order excitations of the HF reference determinant. The CI method is: Variational: Its energy is an upper bound to the ground state NOT size consistent: The energy of a system does not scale with size. For example, two separated molecules will be different if calculated separately and then added, versus calculated together.

Is not:

2X

The reason CI is not size consistent is because truncating the expansion at some level of excitation from the HF reference wave function will exclude some configurations from the composite system that will be included in the fragments. For example, double excitations out of both molecules simultaneously will be a quadruple for the composite CI, and not included in CISD. It is included as 2 times the double excitations in the fragment system.

QC Optimizations and Correlation Lecture 8 Page 2

MBPT methods are an alternative way to systematically correct the Hartree-Fock wave function by mixing in higher order excitations of the HF reference determinant. MBPT is: NOT Variational: Its energy is not an upper bound to the ground state energy. Size consistent: The energy of a system scales with size. E

Order of perturbation

Moller-Plesset many body perturbation theory is a way of correcting the HF ground state for its lack of correlation energy (just as CI was). However, for MP MBPT methods, excited state character to include dynamic correlation is introduced using perturbation theory, rather than mixing in excited states variationally.

Lecture 8 Page 3

MP MBPT

Perturbation theory starts with a zero order wave function and energy and then improves it using a perturbation. In the case of Moller Plesset theory, the zero order Hamiltonian is taken as the sum of Fock Operators:

H HF = fi

i=1 n

Where each Fock operator is the one electron kinetic energy, interaction with the nuclei, and interaction with the average field of its neighbors:

i 2 Z HF fi = A + (i) 2 A riA

The HF ground-state wavefunction is an eigenfunction of HHF with eignvalue E(0) given by the sum of the occupied single electron orbital energies. The perturbation is the difference between the full electronic Hamiltonian and the mean field approximation:

H (1) = H fi

i= 1 n

Lecture 8 Page 4

MP MBPT

The first order correction to the energy is the expectation value of H(1) for the HF wavefunction, which is already included in the HF energy:

E(1) = 0 H(1) 0

The leading correction to the HF ground state energy is then the second order perturbation energy:

( 2)

J H (1) 0 0 H (1) J

E (0) E J

J 0

Here, J refers to HF excited determinants. Thus, perturbation theory mixes in excited state character depending on how the perturbation couples the excited state, and the difference in energy between the excited state and the ground state. Since no truncation is done, MP theory is size consistent. Since the corrections are not mixed in variationally, the method is not variational.

You might notice that Brillouins theorem has something to say about which determinants have non-zero matrix elements and contribute to the second order correction (the doubly excited configurations).

Lecture 8 Page 5

Notes: Perturbation theory has also been used to develop expressions for higher order corrections to the ground state wavefunction. These expressions can be derived in a similar way to the way the lower order corrections are developed (see a general text on Quantum Mechanics) or using graph theory (see Szabo and Ostlund). Second order perturbation theory: MP2 scales as N5. Improves bond energies, and frequencies and transition state energies significantly. MP4 further improves on MP2, although it is highly computationally intensive and generally only practical for small systems.

Lecture 8 Page 6

Unrestricted Wavefunctions

Often times Gaussian (and Quantum chemistry in general) allows one to make a choice as to whether to use a restricted or unrestricted wavefunction. A restricted wavefunction doubly occupies each spatial orbital with two electrons. A restricted open-shell wavefunction is one which doubly occupies the closed shell orbitals of an open shell system. An unrestricted method allows the electrons are not constrained to the same spatial orbitals. For example, UHF H2 would allow each electron to have its own spatial wavefunction, whereas the RHF method would force the two electrons into the same bonding orbital. Unrestricted methods have lower energies than restricted methods (since there are now more variational coefficients). Unrestricted methods are not eigenfunctions of S2, the total spin operator and are often called spin contaminated (how far from a pure spin state the unrestricted method is). This is generally not a big problem. Unrestricted methods should be used for open shell systems. Some unrestricted methods: UHF, UMP2, UB3LYP, etc.

Lecture 8 Page 7

Until now we have discussed methods which start with the Hartree-Fock approximation to obtain spin orbitals, which are then used to construct configuration state functions (using either CI or MBPT). Configuration State Functions: A Slater determinant, or linear combination of Slater determinants. CI or MBPT used to mix in higher order CSFs Doubles Singles Triples

HF In principle CI and many body perturbation theory are exact when expanded to infinite order, however, these methods are both computationally intensive, even when only expanded to the first few terms (CISD, or MP2, for example). Density Functional Theory is an alternative to HF based wave function methods which have become very popular due to there price-performance (they are quite accurate considering their computational efficiency).

Lecture 11 Page 1

DFT

Density Functional Theory is based on the concept that energy of an electronic system is a function of the electron density. The Hohenberg-KohnTheorem (1965) proved that the ground state energy, and all other ground state electronic properties were uniquely functions of the electron density. The basis idea is that the electronic wave function uniquely determines all electronic properties, including the potential energy operator, and the electron density. Consequently, if there is a one-to-one mapping between the wave function, the potential function, and the electron density, we can write the energy as a functional of the electron density.

(r ) (r ) 0

E( ) E(0 )

Problem: the HK theorem doesnt tell us the functional form of the dependence of energy on the electron density.

Lecture 11 Page 2

DFT

The energy is written as the sum of the 1) kinetic energy, 2) the electron-nuclear interactions, 3) the electron-electron interactions and the 4) exchange-correlation energy (unknown).

1 e Een = 1(r1 ) 2 (r2 )dr1dr2 2 r12

2

EXC = EXC ( )

E = Ekin + Een + Eee + E XC

Lecture 11 Page 3

DFT

To determine the energy we use the variational principle to minimize the energy with respect to variational parameters (basis set coefficients typically):

The density is determined using: VXC is determined using:

(r ) = i (r)

i

VXC =

E XC []

The reason DFT is computationally efficient is because integrals over two electrons to determine the coulomb and exchange energy are now replaced by a one electron integral for coulomb, and a functional VXC for exchange.

Also note that DFT explicitly takes into account correlation in the exchange-correlation function. This allows solution similar to the Fock mean field approach although the question is how to determine VXC, and how accurate is it.

Density Functional Theory Lecture 11 Page 4

DFT

Note that just like HF, the wave function (and density) depends on the Hamiltonian, and the Hamiltonian depends on the wave function (as does the density). Thus, like HF DFT methods generally employ a Self-Consistent Field procedure. Choose Structure, Spin and Charge

Concepts determining basis set choice are the same as for wave function methods.

yes

Density Functional Theory Lecture 11 Page 5

One method that has been used for determining the exchange correlation function is to use the LDA. Here, the exchange energy is approximated by the exchange energy per electron of a uniform electron gas with the same density as the local density at point r in the molecule. This gives an analytic form for the exchange energy and potential since the exchange energy of a uniform electron gas can be solved exactly. The problem is that this is not a great approximation for for the exchange energy of a molecule.

Lecture 11 Page 6

Other methods which improve upon LDA have been developed which use more sophisticated descriptions of the exchange correlation functional. BLYP and PW91 are such methods. They are fast, and quite accurate. Energies of stable states and frequencies are accurate. Transition State energies are underestimated. The Becke3LYP (B3LYP) method is similar to BLYP in that it also uses the LYP functional, but it mixes in Hartree-Fock exchange in an amount that is determined empirically by fitting to the G2 molecular set. This method is known as a hybrid since it combines HF and DFT. Since it uses HF it scales with the 4th power of the size of the system. B3LYP improves upon HF, PW91, and BLYP with better energies, especially transition state energies (remember DFT underestimates EA whereas HF overestimates EA). The approximate ordering of methods in terms of errors: EHF > EPW91 > EBLYP > EMP2 > EB3LYP > ECISD > EMP4 > EQCISD > ECCSD The approximate ordering of methods in terms of CPU time: TCCSD > TQCISD > TMP4 > TCISD > TMP2 > TB3LYP > THF > TPW91 > TBLYP

Lecture 11 Page 7

DFT Notes

DFT methods generally: Underestimate activation barriers (2-5 kcal/mol typically for B3LYP). Overestimate frequencies by 1 to 5 percent. Predict good geometries, but using more optimization steps. Are very good methods for d-block transition state metals.

New DFT methods are being developed which have the accuracy of the best methods, yet are faster than B3LYP.

Lecture 11 Page 8

Relative Energies

Relative Energies between stable molecules: Moderately sensitive to basis set Moderately sensitive to level of theory

E(0 180) 3-21G* 6-31G(d) 6-311G(d) 6-31G(d,p) HF 1.77 2.07 2.04 2.07 BLYP 1.90 2.06 1.90 2.04 B3LYP 1.89 2.08 1.94 2.06 MP2 1.72 1.96 1.84 1.98

Practical Points

Lecture 12 Page 1

Bond Energies

Bond Energies: Moderately sensitive to Basis Set Very sensitive to level of theory HF underestimates bond energies, as do most HF based ab initio methods DFT methods often overestimate bond energies C-H Bond Energy in CH4

E(CH3-H) 3-21G* 6-31G(d) 6-311G(d) 6-31G(d,p) HF 86.64 86.56 85.16 87.23 BLYP 113.64 111.89 110.34 112.60 B3LYP 114.24 112.84 111.27 113.50 MP2 101.08 103.90 103.39 108.99

E(H-H) 3-21G* 6-31G(d) 6-311G(d) 6-31G(d,p) HF 81.93 81.80 80.58 84.63 BLYP 110.21 109.41 107.63 111.08 B3LYP 110.43 109.77 108.13 111.69 MP2 92.78 92.67 91.78 101.15

Practical Points

Lecture 12 Page 2

Transition State Energies: Activation barriers are generally underestimated by DFT methods Overestimated by HF and HF based ab initio methods Barrier is reduced by increasing the basis set Barriers are very sensitive to level of theory Possibly the most difficult property to calculate accurately. Silane Dehydrogenation Activation Barrier:

Practical Points

Lecture 12 Page 3

Vibrational Frequencies

Vibrational Frequencies: Moderately affected by basis set Moderately affected by level of theory

BLYP B3LYP MP2 Si-H Sym Stretch modes HF 3-21G* 2405.762 2211.433 2273.865 2351.2716 6-31G(d) 2396.526 2183.956 2250.447 2319.7671 6-311G(d) 2361.178 2172.692 2235.81 2293.3653 6-31G(d,p) 2368.431 2176.732 2239.663 2343.3492

Practical Points

Lecture 12 Page 4

Geometries

Molecular structure is not usually very sensitive to basis sets. However, in strained systems, and transition states basis sets may affect the structure moderately. Molecular structure is usually not very sensitive to level of theory. HF, for example gives quite accurate geometries for most systems. Again, transition state structures may be more sensitive to level of theory. Note: In various cases the level of theory wont be appropriate to the molecule: For example, HF will not describe transition metals well. In those cases structure will be very sensitive to method.

Practical Points

Lecture 12 Page 5

Basis Sets can often be Split to maximize the accuracy of the method on the chemically active part of the molecule. Add additional functions to atoms that have bonds being stretched, or broken Add additional functions to atoms that are donating or accepting charge Note: Adding additional functions to DFT may (usually) make activation barriers worse.

Note: Splitting the basis set and Split Valence basis sets are not the same thing.

Practical Points

Lecture 12 Page 6

Constrained Optimizations

In many cases, geometry optimizations should be done with constraints. This often includes cases where the cluster represents a portion of a larger molecule where the rest of the molecule added rigidity to the structure. Constraints can also be used to narrow a transition state search and scan potential energy surfaces.

Practical Points

Lecture 12 Page 7

Systematic Corrections

Many of the errors inherent in the approximations needed to make ab initio methods practical are systematic. Various correction methods have been developed to estimate the size of the errors due to these approximations, and to determine approximate corrections for the various methods. Corrections have been developed for: vibrational frequencies basis set truncation correlation energy Each of these corrections can be applied to a specific calculation individually, or combined to form a method, for example the G2 method.

Systematic Corrections

Lecture 13 Page 1

Vibrational Frequencies

Scaling factors can be derived to correct vibrational frequencies. This is done by performing calculations on small molecules with well characterized frequencies similar to the molecule of interest to obtain a multiplicative scaling factor:

S=

j (exp) 1 J j j (theory)

The best estimate for the experimental frequency of the unknown frequency is then:

j (scaled) = S j (theory)

Zero point energy corrections can also be based on scaled frequencies. Note that relative energies will not be very sensitive to scaling because both states will be upward corrected by the ZPE correction.

Systematic Corrections

Lecture 13 Page 2

All calculations must be performed at a particular basis set. The larger the basis set, the more accurate the calculation (usually). However the calculation also becomes more expensive with bigger basis sets. Various studies have noted that the largest errors in calculating total energies usually come from the finite size of the basis set. We also know that successively increasing the size of the basis set leads to smaller and smaller improvements in energy. Thus, the asymptotic convergence of the total energy with basis set size can be used to determine an extrapolated estimate for the energy for the complete basis set. Various schemes have been developed to do this and all involve a series of calculations with different basis sets (and sometimes at higher level methods) to determine the extrapolation.

Systematic Corrections

Lecture 13 Page 3

Not only can correction schemes be developed to determine the effects of basis set truncation, but extrapolation to higher order methods that include more correlation energy can also be performed. Extrapolation schemes consist of a series of calculations at higher levels of theory to estimate the convergence point of the total energy with level of theory. A series might include HF, MP2, MP4 and QCISD. HF is used as the base method. MP2 is used to include second order corrections to the energy. MP4 is used to approximate higher order corrections. QCISD is used to determine how well MP4 approximated the higher order corrections and thus how to include the higher order corrections. The best calculations would involve performing high level methods (say QCISD or CCSD) at very large basis sets. Because it is impractical to do this calculation we approximate the best calculation by correcting for both basis set and correlation energy together. Several methods have been developed to do this. CBS Methods: CBS-4 and CBS-Q G1, G2, and G3

Systematic Corrections

Lecture 13 Page 4

CBS Methods

CBS: Complete Basis Set extrapolation methods. CBS-4 1) HF/3-21G(d) opt for geometry. 2) HF/3-21G(d) freq for ZPE. 3) HF 6-311+G(3d2f,2p) For base energy. 4) MP2/6-31+G with basis set extrapolation to correct basis set and correlation to 2nd order. 5) MP4 /6-31+G(d,p) to estimate higher order corrections. The CBS-Q method is similar: CBS-Q 1) MP2/6-31G(d) opt for geometry. 2) HF/6-31G(d) freq for ZPE. 3) HF 6-311+G(3d2f,2p) For base energy. 4) MP2/6-31+G with basis set extrapolation to correct basis set and correlation to 2nd order. Basis set extrapolation done with more points that CBS-4 5) MP4 /6-31+G(d,p) and QCISD(T) to estimate higher order corrections. Higher order corrections for spin contamination and core correlation often added.

Systematic Corrections

Lecture 13 Page 5

The G2 Method

The G2 method is similar to the CBS-Q and CBS-4 methods and also involves a series of calculations: 1) HF/6-31G(d) opt for geometry. 2) HF/ 6-31G(d) freq for ZPE. 3) MP2/6-311G(d,p) opt from HF opt in 1. Use this geometry for all later jobs. 4) MP4/6-311G (d,p) Single point for base level energy. 5) MP4/6-311+G (d,p) Single point to correct base for diffuse functions 6) MP4/6-311G (2df,p) Single point to correct base for polarization functions (set to zero if greater than from step 5) 7) QCISD(T)/6-311G(d,p) Correction for correlation energy 8) MP2/6-311+G(3df,2p) Correct for non-additive corrections in 5, and 6 9) High level corrections and Spin correction

Systematic Corrections

Lecture 13 Page 6

Configuration Interaction methods truncate the CI expansion and a certain excitation, for example CISD truncates the CI expansion to include the Hartree Fock ground state determinant and singles and doubles excitations from the HF reference configuration.

rs = c0 0 + Tar 0 + Tab 0 a ,r ab , rs

The finite truncation leads to the problem of size consistency where the CI energy does not scale with the size of the system.

For example, the energy of two isolated He atoms should be the same as two times the energy of each He atom calculated separately. This is not true for CISD.

E(2He) 2E(He)

The finite truncation leaves out certain configurations which are physically simultaneous excitations of each fragment which are formally higher order excitations.

Lecture 14 Page 1

b b b r r rs rs + caTa a + cabTab a =c a a b a b 0 a b ar ar

HF

Singles

+

c c c c

Doubles

a =c a 0 a a

b b b b

HF

c c c c

d a d a + crT r a a d a ar d a

b b b b

d a d a + c rs T rs d ar ab ab a d a

b b b b

c c c c

d d d d

Singles

Doubles

Notice that only half (2 of 4) of the occupied orbitals are replaced at the doubles level.

Lecture 14 Page 2

As the number of He atoms grows, the percentage of orbitals excited at the singles and doubles levels decreases. Thus, the CISD energy approaches the HF energy as the system becomes infinitely large. HF Single Double

This is formally a double excitation, although most of the He is in the HF ground state.

QCISD and CCSD Methods

This is also formally a double, although most of the He is in the HF ground state.

Lecture 14 Page 3

QCISD

QCISD is a method which similar to CISD, but which adds excited state determinants which are formally triples, and quadruples but which arise due to simultaneous singles and doubles or simultaneous doubles excitations. The terms that are added are: Disconnected Triples:

T1T2

This term accounts for triples that arise due to simultaneous singles and doubles excitations.

Disconnected Quadruples:

1 (T2 )2 2

This term accounts for quadruples that arise due to simultaneous doubles excitations. The factor of one half is included to remove the double counting of pairs of doubles. These are the terms which lead to size consistency.

Lecture 14 Page 4

QCISD

Notes: The QCISD method is extremely computationally intensive. This should not be used on systems with over 6-8 heavy atoms on a fast workstation. To achieve the best accuracy, QCISD should be basis set extrapolated. The QCISD(T) method involves adding direct or connected triples to QCISD. This leads to a large improvement in energies, especially for transition states and excited states. QCISD is intermediate to the couple-cluster CCSD method in that it includes many of the same terms included in CCSD, but not all the CCSD terms. QCISD approaches the accuracy of CCSD, but is somewhat less computationally intensive.

Lecture 14 Page 5

The coupled cluster method is one of the most accurate methods available today. It also involves adding terms left out in the CI truncation to make the method size consistent. However, it does this using the wave function:

= exp T 0

The operator T is just the sum of all the excitation operators:

()

T = T1 + T2 + T3 + ...

The T operators produce excited configuration determinants from lower order determinants and include unknowns for the relative amount of the configuration to be included in the overall wave function (these are the variational parameters equivalent to the CI expansion coefficients. The CCSD method uses the wave function:

Note that this form includes all disconnected triples and quadruples through the terms;

T1T2

1 TT 2 2 2

1 T1T1T1 3

1 T1T1T2 2

Lecture 14 Page 6

CCSD

As in QCISD(T), we can also include triples in approximately using the CCSD(T) method. Triples could also be included exactly using:

= exp T1 + T2 + T3 0

This is called CCSDT.

Coupled Cluster theory has become the method of choice when very high accuracy is required. Beware that this method is extremely expensive, but is appropriate when very small systems are to be studied at high accuracy.

Geometries and frequencies are not usually computed at the CCSD level due to the computational expense: Typically the CCSD energies are computed at geometries obtained with lower level methods.

Lecture 14 Page 7

## Mult mai mult decât documente.

Descoperiți tot ce are Scribd de oferit, inclusiv cărți și cărți audio de la editori majori.

Anulați oricând.