Quantum Mechanics Calculations II Noel M. OBoyle Apr
Quantum Mechanics Calculations II Noel M. OBoyle Apr 2010 Postgrad course on Comp Chem Overview of QM methods Molecular mechanics Quantum mechanics (wavefunction)
Quantum mechanics (electron density) Including correlation Speed/Accuracy HF (ab initio) Semi-empirical Forcefields DFT
Semi-empirical methods Time required for HF scales as N4 calculation of one-electron and two-electron integrals Semi-empirical methods speed things up by Considering only the valence electrons Using only a minimal basis set Setting some integrals to zero, only N2 to evalute Use simple formulae to estimate the values of the remaining integrals The evaluated integrals are parameterised based on calculations or experimental results (hence semiempirical) This compensates (to some extent) for the simplifications employed Implicitly includes electron correlation neglected by HF
MNDO/d (Thiel, Voityuk, 1996) AM1/d (Voityuk, Rosch, 2000) RM1 (Rocha, ..., Stewart, 2006) PM6 (Stewart, 2007) INDO Compared to CNDO, INDO allows different values for the onecentre two-electron integrals depending on the orbital types involved (s, p, d, etc.) INDO more accurate than CNDO at predicting valence bond angles but tends to be poor overall at predicting molecular geometry ZINDO/S is a parameterisation of INDO using spectroscopic data First described by Ridley, Zerner (1973) Since then, Zerner and co-workers extended to include most of the
elements in the periodic table ZINDO/S still widely used however for prediction of electronic transition energies and oscillator strengths, particularly in transition metal complexes (UV-vis spectrum) ZINDO/S results can be of comparable accuracy to those obtained with the more rigorous (slower) TD-DFT method NNDO Compared to INDO, NNDO allows different values for the two-centre twoelectron integrals depending on the orbital types involved (s, p, d, etc.) AM1 Austin Model 1 Dewar, Zoebisch, Healy, Stewart (1985) PM3 Parameterised Model 3 Stewart (1989) Essentially AM1 with an improved parameterisation (automatic rather than
manual, large training set) Both AM1 and PM3 are still widely used PM6 Stewart (2007) Main objective to improve handling of hydrogen bonds PM6 was included in Gaussian09 http://openmopac.net/Manual/accuracy.html Overview of QM methods Molecular mechanics Quantum mechanics (wavefunction)
Quantum mechanics (electron density) Including correlation Speed/Accuracy HF (ab initio) Semi-empirical Forcefields DFT
Handling electron correlation Hartree-Fock (HF) theory HF theory neglects electron correlation in multi-electron systems Instead, we imagine each electron interacting with a static field of all of the other electrons Electron correlation can be handled by including multi-determinants Construct the wavefunction from some linear combination of the HF ground state, plus the singly excited determinants (S), the doubly excited (D), the triply excited (T), etc.
Image Credit: Introduction to Computational Chemistry, Frank Jensen, Wiley, 2nd Edn. Handling electron correlation Configuration interaction (CI) Use the variational principle to determine the coefficients that minimise the energy of the multi-determinant wavefunction Full CI => use all possible determinants (100% of correlation energy found, but too expensive for all but the smallest system) CI with Singles and Doubles (CISD) scales as N6 can be used with medium size molecules and recovers 80-90% of the correlation energy Moller and Plesset used Many Body Perturbation Theory The unperturbed state is the HF energy, while higher order perturbations involve corrections to the unperturbed state to greater and greater accuracy
MP2 is the first correction, then MP3, etc. - scales as N5 for MP2, N6 for MP3, etc. Not variational (can overestimate the correlation energy) and does not converge smoothly with higher order (oscillates) Other methods: Multi-configuration SCF, Coupled-cluster theory HF << MP2 < CISD < MP4 (SDQ) < ~CCSD < MP4 < CCSD(T) Dunning et al developed basis sets specifically for recovering correlation energy cc-pVDZ, cc-pVTZ, cc-pVQZ, cc-pV5Z (Valence Double Zeta, Triple, etc...) cc for correlation consistent, p for polarised
Overview of QM methods Molecular mechanics Quantum mechanics (wavefunction) Quantum mechanics (electron density) Including correlation Speed/Accuracy
HF (ab initio) Semi-empirical Forcefields DFT Density Functional Theory (DFT) Walter Kohn - Nobel Prize in Chemistry 1998 "for his development of the density-functional theory Based on the electron density rather than the wavefunction DFT optimises the electron density while MO theory (HF, etc.) optimises the wavefunction
Components of the Hamilitonian are expressed as a function of the electron density (), itself a function of r Function of a function = functional Composed of an exchange functional and a correlation functional Variational principle can also be shown to hold Hohenberg-Kohn Variational Theorem The correct electron density will have the lowest energy The approach used to solve for the density is the KohnSham (KS) Self-consistent Field (SCF) methodology Density Functional Theory (DFT) Local spin density approximation (LSDA) Functional values can be calculated from the value of at a point Exchange functionals: LDA, Slater (S), X
Correlation functionals: VWN Generalised gradient approximation (GGA) Functional values use gradient of Exchange functionals: B (Becke), B86, PBE Correlation functionals: P86, PW91, LYP (Lee, Yang, Parr) Name of DFT method is made by joining the exchange and correlation functionals into one word E.g. B + PW91 = BPW91 Hybrid DFT methods Includes some HF exchange not pure DFT B3 - Beckes 3-parameter functional for exchange (includes some HF, LDA and B) Also some one-parameter models: B1, PBE1, mPW1
B3LYP is the most popular DFT functional to date DFT compared to MO theory DFT is an exact theory (unlike HF which neglects electron correlation) but the functionals used are approximate DFT calculations scale as N3 More rapid basis-set convergence Much better for transition metal complexes Known problems with DFT Not good at dispersion (van der Waals) H-bonds are somewhat too short overdelocalises structures Hard to know how to systematically improve DFT
results In MO, can keep increasing the basis set and level of theory Handling very heavy elements Two main problems handling very heavy elements Lots of electrons => lots of basis functions (remember, HF scales as N 4) C has 6 electrons, Au has 79 Relativistic effects start to come into play Solution Replace the core electrons with a single function that represents reasonably accurately (but much more efficiently) the combined nuclear-electronic core to the remaining electrons Effective Core Potential (ECP), or pseudopotential Relativistic effects can be folded into the ECP
Large-core ECPs include everything but the outermost valence shell The remaining electrons are handled with basis functions as before Small-core ECPs include everything but the two outermost valence shells (more accurate) Examples: LANL (Hay, Wadt, 1985), Stuttgart/Dresden (Dolg et al, 2002) When used in practice, the basis functions are also specified, e.g. LANL2DZ implies the LANL ECP with a double-zeta (split-valence) basis set LANL2MB implies the LANL ECP with a minimal basis set (single-zeta) Geometry Optimisation Energy minimisation E = f(x1, y1, z1, ..., xn, yn, zn) General principal:
Starting from an initial geometry, find the molecular geometry that minimises the energy of the molecule Note: local optimisation (not global) Only goes downhill along PES (potential energy surface) from the initial geometry This implies, for example, that a cyclohexane boat conformation wont optimise to a chair (although the latter is the more stable form) Minimisation of a multivariate function is a well-studied problem Use the slope (1st derivative of E) to determine in which direction to move: Steepest descent, Conjugate gradients Some methods also use the 2nd derivative: Newton-Raphson When you get to a point where the 1 st derivative is zero, you need to verify that its not a saddle-point Calculate the vibrational frequencies and check that none is imaginary
Also methods to find transition structures (saddle points), and methods to identify a reaction path between reactant, transition state and product Vibrational frequency calculation For a particular molecular geometry, there is a particular energy Potential energy surface (PES) Its possible to solve Schrodingers equation for nuclear motion (instead of electronic motion) Harmonic oscillator approximation Represent molecular vibrations as perfect springs (restoring force is proportional to distance from equilibrium) With this approximation, Schrodingers equation Gives frequencies and normal modes
Force constants of frequencies calculate from second derivative of the energy with respect to the vibrational motion Can visualise the molecular vibrations that give rise to particular peaks in the IR (or Raman) Real vibrations are not harmonic oscillators The calculated frequencies are usually too large by a largely constant factor The value of the factor has been determined for several LOTs and BSs and can be used to scale the calculated frequencies If you are not at a minimum on the PES, you will obtain one or more imaginary frequencies (vibrations with a negative force constant) Thus its a good idea to carry out a frequency calculation after a geometry optimisation to verify you are at a true minimum and not at a .... Transition states have a single imaginary frequency (i.e. they are a minimum in every direction except the one that joins the reactant and product, where they are at a maximum see picture on next page)
http://cse-online.net/twiki/bin/view/Main/KineticTheory Zero-point vibrational energy When comparing the energies of different molecules, you need to correct for ZPVE ZPVE is the internal energy a molecule has (even at the zero-point, 0K) due to its vibrations This can be calculated from the vibrational frequencies In other words, you need to carry out a frequency calculation To the extent that the harmonic oscillator approximation affects vibrational frequencies, the ZPVE is also affected (and similarly, scaling can
also improve the results) Calculating Ionisation Potential and Electron Affinitiy Koopmans theorem: IP is the negative of the energy of the HOMO Note: The energies of the occupied orbitals are always negative - the HOMO is the least negative Something of an approximation but works quite well Ignores the effect of electron relaxation in the ionised product Can use Koopmans theorem for EA also EA is the negative of the energy of the LUMO But the error is greater here, and a better approach is the SCF approachSCF approach
Calculate the difference between the energy of the molecule with and without the extra electron Virtual orbitals These are the high energy unoccupied orbitals that arise in a comp chem calculation As they do not contain electrons, they do not contribute to the overall energy of the molecule Hence, neither their shapes nor their energies were optimised during the SCF procedure Despite this, they can be used for quantitative arguments HF and DFT virtual orbitals tend to have the same shape but their energies differ HF virtual orbitals experience the potential that would be felt
by an extra electron being added to molecule As a result, they tend to be too high in energy and diffuse compared to KS virtual orbitals (from DFT) Examples from this weeks JACS Zheng et al, J. Am. Chem. Soc., 2010, 132, 5394. Sarma, Manna, Minoura, Mugesh, J. Am. Chem. Soc., 2010, 132, 5364. Hong, Tanillo J. Am. Chem. Soc., 2010, 132, 5375. Epping et al, J. Am. Chem. Soc., 2010, 132, 5443.
Modern Chemistry Chapter 6 ... Illustration: A + B A+ + B- Covalent Chemical bond resulting from the sharing of valence electrons between two atoms In a pure covalent the electrons are shared equally between the two atoms (called nonpolar...
For example, the CPR was given a large amount of land, about 100 000 square km, in exchange for building the new railway to accommodate for immigrants coming in. Spreading the Word. Laurier got the word out by: 1. Putting...
The DD Form 1348-1A is an approved form of sub-custody for non-expendable A&E. It is the preferred method of sub-custody for security, dummy, and inert A&E from the Ammunition Chief to the Armory. Reference: MCO 8010.13, enclosure (1), chapter 5....
or model the inquiry (or both!). Developing these inquiry skills . ... Photos by Rick Bein, Gray Tappan, and Phil Gersmehl. Teachers who saw this presentation at a workshop. or downloaded it from our internet site have permission ...
Projectiles move in TWO dimensions a projectile moves in 2-dimensions, Horizontal -applied force and Vertical- gravitational force Combining the Components Together, these 2 components produce what is called a trajectory or path. This path is parabolic in nature. You must...
Synonym-boisterous. The salesman's . raucous. voice was heard throughout the whole store. It's important to be receptive to new ideas and opinions. receptive. Adj- willing to listen to new ideas and opinions. Synonym-open-minded. Sometimes my friends aren't too .
Neolithic-New Stone Age-Skulls were painted and used for ritual, ... can be economic (jobs and wealth), social (popularity) Neolithic-New Stone Age-Markers of civilization. 2. Stable Food Supply. When a society has enough food so it . can. survive,