| 1 |
theory |
Course overview; syllabus; requirements; goals; research paradigm shift |
1. Basic rules about the course; 2. explain the Syllabus, including textbooks; 3. state the Prerequisites and Course goals; 4. What is electronic structure of molecules? 5. Shift of research paradigm; 6. The Nobel history about electronics structure of molecules; 7. show an example of a scientific debate regarding models; 8. Simulation/theory vs. experiment 9. discuss in details about model and modeling; 10. Topics not covered; |
1. No plagiarism is allowed in the homework assignments!. 2. 1/2 ES-related Nobel laureates are Jews (scientific critical thinking is crucial in Jewish education); 3. Use an example to show the scientific debate and try to emphasize the critical thinking. |
| 2 |
theory |
Concepts related to ESM; models; ab initio; semiempirical; ES calculation; Bottleneck; first principles; computational chemistry; modeling |
1. clarify a few concepts of ESM including theoretical chemistry, computational chemistry, quantum chemistry, electronic structure calculation, as well as molecular modeling, molecular mechanics, molecular dynamics; 2. introduce models at different levels: plastic, molecular mechanics; semiempirical, ab initio, first principles method; 3. brief discussion on electronic structure calculation. Its bottleneck; the general approach to simplify Shrondinger eq.; 4. introduce modeling techniques; ES procedure; 5. summarize the contents of the first and second hours |
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| 3 |
theory |
ES research; MD simulation; right questions; advantage; disadvantage; computation environment; resources |
1. Anatomy of a computational research group. What can we do? Reaction mechanism/pathway/transition states/bizarre electronic structure and its regulation/excited states/transport properties/magnetic interactions/PBC/2D/interface... 2.ES vs. MD their distinction and fusion. ab initio MD; Semiempirical/Tight binding DFT; ReaxFF; coarse grained; 3. discovering chemistry AIMD; 4. what can ES calculation do? stability and reaction mechanism? 5. ask the right questions. relative property/ trend/gas phase/ground state 6. advantage of ES calculation 7. disadvantage of ES calculation 8. status of ES study 9.computation environment. Hardware vs. Software; in-school service and commercial service; Resources online, training, books, journals. 10. summary |
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| 4 |
theory |
Gaussian; Gaussview |
1. Introducing Gaussian and Gaussview. 2. Show the general procedure of setting up and running a computation job. 3. How to basically understand the output file. |
Introduce China-based electronic structure calculation software develop teams. Xiamen University (Wu Xin team), Shandong University (Liu Wenjian team), Jilin University (Ma Yanming team). |
| 5 |
theory |
review quantum mechanics; Part I; Particle in a potential |
review of quantum mechanics. 1. History (Planck, Einstein, De Broglie; Bohr, Heisenberg, Schrodinger); 2. matter wave duality; stationary state; Well-behaved wavefuntions; kinetic vs. potential energy; 3. quantization: macroscopic item and microscopic particle; 4. Particle in a ring; exp. realization/example 5. Particle in a box; exp. realization |
Scientists facing political bifurcation (Bohr vs. Heisenberg), how to choose. |
| 6 |
theory |
review QM2; Particle in a 3D box; Quantum confinement; Potential; free particle; Postulates; |
Review of QM 1. Particle in a 3D box; wavefunction/energy level/degeneracy; exp. realization; 2. Particle in a 0D box; Quantum dots; quantum confinement; 3. Particle in a potential; 4. Free particle and its derivatives; 5. Postulates of QM |
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| 7 |
theory |
Single point energy; input; output |
Single point energy 1. what is single point? configuration = single point on potential energy surface. 2. prepare Gaussian input file 3. read Gaussian output file 4. plot molecular orbitals 5. plot NBOs 6. charge Mulliken vs. NPA 7. NBO (localization) vs. MO (delocalization) 8. Benzene's orbitals 9. Constants and units |
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| 8 |
theory |
Electronic structure of atoms; Hydrogen atom |
Electronic structure of atoms 1. Schrodinger equation of Hydrogen atom; Angular & radial components 2. Dirac bra-ket notation; Complete orthonormal basis; 3. Variational principle 4. Basis functions; 5. Secular equations 6. Spin |
How to advise students and build a strong research team? Example of Neils Bohr. |
| 第 9 学时 |
理论 |
Basis functions: beyond orbitals |
1. Basis functions; 2. Beyond the H-like orbital approximation; 3. Beyond the orbital approximation 4. Secular equations 5. Spin 6. Is orbital observable? 7. bond order calculation |
Criticize the statements in top journals "we observed orbitals". |
| 第 10 学时 |
理论 |
Molecular orbital theory; The Hartree-Fock method |
The Hartree-Fock method 1. The problem of many electrons 2. Hartree atom; 3. Self-consistent field approach |
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| 第 11 学时 |
理论 |
The Hartree-Fock method; Part 2; Spin |
The Hartree-Fock method 1. Pauli principle. e.g. He atom 2. Slater determinants. e.g. He atom in excited state 3. Coulomb integral 4. Exchange integral. 5. Triplet vs singlet. 6. Nuclear spin isomers |
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| 第 12 学时 |
理论 |
Examples of triplet and singlet; atom and molecule |
triplet and singlet 1. Compute C atom 2. O2 molecule. 3. H self-interactions. |
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| 第 13 学时 |
理论 |
The Hartree-Fock method; Part 3; Electron Correlation |
The Hartree-Fock method 1. Hartree-Fock equation 2. HF-Slater model 3. Local density approximation. Approximating the Fermi hole 4. more on exchange potential 5. more on LDA 6. Correlation |
Hybridizing DFT and HF theories leads to unexpected accurate results, which in analogy can help us understand the success of the mixed economic policy of China. |
| 第 14 学时 |
理论 |
Electronic structure of molecules; Molecular orbital method 1 |
Electronic structure of molecules 1. Born-Oppenheimer approximation; H2 molecule; PES 2. Linear Combination Atomic Orbitals; HF/MO orbitals; basis sets 3. Fock equation; Fock operator |
(1). The collective behavior of a lot of microscopic particles can be equated to the simple behavior of a quasi-particle. So does human. E.g. stereotype a group of people. (2) To a certain extent, the definition of oneself is not by oneself only, but by a number of people's (current and future) view on that individual. Therefore, individual lives in the (mind of) group. |
| 第 15 学时 |
理论 |
Molecular orbital method; Part 2; Single Point Summary |
MO method 1. Roothaan-Hall equations 2. Fock matrix and overlap matrix 3. Intergrals for the Fock matrix 4. Solving the Roothaan-Hall equations 5. SCF done 6. Comments on the Roothaan-Hall equations 7. Single point energy summary |
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| 第 16 学时 |
理论 |
Semi-empirical methods；Open-shell systems；SCF details |
1. Semi-empirical methods; EHT; NDO; NDDO 2. Open-shell systems; RHF; UHF/ROHF 3. SCF details 4. Single point calculation: NMR |
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| 第 17 学时 |
理论 |
Basis set; Part 1; Pople; Dunning |
Basis set 1. Gaussian type orbitals 2. Pople basis sets 3. Dunning basis set |
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| 第 18 学时 |
理论 |
Basis set; Part 2; ECP; Pseudopotential |
Basis set 1. Basis set effect 2. Pseudopotentials or Effective Core Potentials 3. Population analysis |
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| 第 19 学时 |
理论 |
Potential energy curves/surfaces; BOA; Nuclear motion |
Potential energy curves/surfaces 1. Configurations, energy levels, and stable states 2. Potential energy curves; examples of X2 molecules 3. Typical potential energy curves 4. Multidimensional potential energy surfaces 5. Model potential energy surface 6. Born-Oppenheimer approximation 7. Nuclear motion on the PES |
PES is where the nuclei are and they stick to PES unless excited by the external fields. People are similar. Without "good environment", people stay on their ground state PES and never above their normal capacity. Only when the external stimulation takes place, the person can move up to the next energy level. However, unfortunately, transient high energetic state won't last. Everyone has to return to one's ground state PES. |
| 第 20 学时 |
理论 |
Time-independent molecular properties; Evaluating derivatives; Exploring PES |
Time-independent molecular properties 1. Geometrical derivatives 2. Interaction with an external electric field 3. Properties from energy derivatives 4. Evaluating derivatives 5. Exploring PESs |
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| 第 21 学时 |
理论 |
Exploring PES; relaxed scan; rigid scan |
Exploring PESs 1. rigid scan 2. relaxed scan 3. PES scanning plot 4. Key points on the PES plot |
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| 第 22 学时 |
理论 |
Geometry optimization; energy gradient; Hessian matrix |
Geometry optimization 1. Potential energy surface 2. B-O approximation & energy derivatives 3. Energy gradients 4. Hellmann-Feynman theorem 5. Pulay forces 6. Second-derivatives of energy 7. Finite difference |
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| 第 23 学时 |
理论 |
Optimization algorithms; Convergence in optimization |
Optimization algorithms 1. Steepest descent 2. Conjugate gradient 3. The Newton-Raphson method 4. Quasi-Newton methods 5. Direct Inversion in the Iterative Subspace(DIIS) 6. Convergence criteria 7. Convergence in optimization |
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| 第 24 学时 |
理论 |
Optimization procedure; Coordinate systems; Quantum harmonic oscillator |
Optimization procedure 1. Method comparison 2. Efficient coordinate systems 3. H-F performance for geometry optimizations 4. Quantum harmonic oscillator 5. Mass-weighted Hessian |
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| 第 25 学时 |
理论 |
Normal modes; scale factor |
Normal modes 1.Summary of normal modes 2. Vibrational frequency 3. Scale factor |
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| 第 26 学时 |
理论 |
Transition states; TS/QST2/QST3 |
Transition states 1. coordinate dragging 2. Hessian-based optimization methods 3. TS/QST2/QST3 4. Comparison of TS optimization |
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| 第 27 学时 |
理论 |
Testing transition structures; IRC; optimization problems |
Testing transition structures 1. frequency analysis 2. Intrinsic reaction coordinates 3. Geometry related energy derivatives in Gaussian 4. Geometry optimization: problem |
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| 第 28 学时 |
理论 |
Thermochemistry; ZPE; isotope effect; reaction energy |
Thermochemistry 1. temperature and pressure 2. ZPE and thermo energy 3. isotope effect 4. Reaction energies |
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| 第 29 学时 |
理论 |
Solvation; Explicit solvent models; Implicit solvent models |
Solvation 1. From vacuum to liquid 2. Born-Haber cycle 3. Explicit solvent models 4. QM/MM 5. MC/MD 6. Implicit solvent model 7. The Poisson equation 8. The Born equation 9. Polarizable continuum model 10. Generalized Born approximation 11. Electrostatic and non-electrostatic components 12. Comments on continuum solvation models |
Environment on a person is as important as solute molecules to solvent molecules. |
| 第 30 学时 |
理论 |
Excited states; Absorption; Emission; Solvatochromism |
Excited states 1. Ground state and excited state configurations 2. Koopmans theorem; 3. ΔSCF 4. Configuration interaction 5. CIS/ZINDO 6. MC-SCF 7. TDDFT 8. Geometry of ES 9. Emission 10. Solvatochromism |
Personal plan should complies with the needs of nation, just as the photons with fit wavelengths can be absorbed or emitted. |
| 第 31 学时 |
理论 |
Electron Correlation; CI; MPn; DFT; model chemistry |
1. Electron Correlation 2. Configuration Interaction 3. Size extensivity 4. Perturbation methods 5. Coupled-cluster methods 6. Ab initio solution of the Schrodinger equation 7. DFT 8. Model chemistries |
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| 第 32 学时 |
理论 |
Final review; Q&A |
Brief review of the entire course 1. MO method/DFT/correlation 2. explore PES/geometry optimization/TS 3. solvation and excited states
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