《分子电子结构》研究生课程教学资源（Electronic Structure of Molecules）ESM-1-intro

Lecturesandlabs1. Lectures and computer labs1. In class, laptops, 20-30 min in classes2.Course materials will beposted on百度网盘、U盘3.Questions1. In class: raise your hand;2. After class: chaowu@xjtu.edu.cn (preferred) QQ:140180893.Office hourby appointment曲江校区西二楼A1044. Rules & grades:1. Attendance (20%, missing >3 sessions, grade = 0 point)2. Project (80%; related to your group's research; a reportin English is required; computational results, includinglog files)2

2 Lectures and labs 1. Lectures and computer labs 1. In class, laptops, 20-30 min in classes 2. Course materials will be posted on 百度网盘、U盘 3. Questions 1. In class: raise your hand; 2. After class: chaowu@xjtu.edu.cn (preferred) QQ: 14018089 3. Office hour by appointment 曲江校区西二楼A104 4. Rules & grades: 1. Attendance (20%, missing >3 sessions, grade = 0 point), 2. Project (80%; related to your group’s research; a report in English is required; computational results, including log files)

SyllabusWeek 1-2Courseoverview;introducing Gaussian&GaussviewWeek 3-4ReviewQM; singlepoint energycalculationWeek5-6Hatom, Hartree-Fock method; orbitalanalysisWeek 7-8Variousapproximations(BOA,LCAO,Semi-empiricalmethods,basisset);related calculationsWeek9-10Potentialenergysurface/scan,geometryoptimization (transitionstate),vibrationWeek11-12Modelchemistry,thermochemistry,scFconvergency;oneelectronproperties,electron correlation, densityfunctionaltheoryWeek13-14Solvation,excitedstatesWeek15-163Comprehensiveexamples,selectedtopics,review

Syllabus 3 Week 1-2 Course overview; introducing Gaussian & Gaussview Week 3-4 Review QM; single point energy calculation Week 5-6 H atom, Hartree-Fock method; orbital analysis Week 7-8 Various approximations (BOA, LCAO, Semi-empirical methods, basis set); related calculations Week 9-10 Potential energy surface/scan, geometry optimization (transition state), vibration Week 11-12 Model chemistry, thermochemistry, SCF convergency; one electron properties, electron correlation, density functional theory Week 13-14 Solvation, excited states Week 15-16 Comprehensive examples, selected topics, review

Abouttextbooks1. James B. Foresman, Aleen Frisch. ExploringChemistry with Electronic Structure MethodsWallingford, USA: Gaussian, 2015中文版：探索化学的奥秘：电子结构方法2. Frank Jensen. Introduction to ComputationalChemistry. West Sussex, UK: Wiley, 2017

About textbooks 4 1. James B. Foresman, Aleen Frisch. Exploring Chemistry with Electronic Structure Methods. Wallingford, USA: Gaussian, 2015. 中文版：探索化学的奥秘：电子结构方法 2. Frank Jensen. Introduction to Computational Chemistry. West Sussex, UK: Wiley, 2017

Prerequisites1.Undergrad Pchem/Structural chemistry or theequivalent;2. Introduction to Quantum Chemistry, desirablebut not required;3.Minimum math to present the modelingmethods and underlying theory;4.Familiarity with Windows is desirable5

Prerequisites 5 1.Undergrad Pchem/Structural chemistry or the equivalent; 2. Introduction to Quantum Chemistry, desirable but not required; 3.Minimum math to present the modeling methods and underlying theory; 4. Familiarity with Windows is desirable

Coursegoals1. Understand the capabilities, limitations, and reliabilityof various molecular modeling methods (esp. electronicstructure calculations);. Provide somebackground onthetheoretical andcomputational methods used in molecular modeling2. Provide hands-on experience with basic molecularmodeling techniques;· Gaussian 16 and Gaussview 63. Grasp general strategy for conducting computationalchemistry research6

Course goals 6 1. Understand the capabilities, limitations, and reliability of various molecular modeling methods (esp. electronic structure calculations); • Provide some background on the theoretical and computational methods used in molecular modeling 2. Provide hands-on experience with basic molecular modeling techniques; • Gaussian 16 and Gaussview 6 3. Grasp general strategy for conducting computational chemistry research

Shiftofresearchparadigm1998 Nobel Prize in Chemistry with one half toProfessor JOHN A.POPLE· Pople has developed quantum chemistry into a toolthat can be used by the general chemist and hasthereby brought chemistry into a new era whereexperiment and theory can work together in theexploration of the properties of molecular systems.Chemistryis no longer a purely experimental scienceIn other words, theory/computation/simulation hasbecome experiment in silico;Not only for chemistry: physics, materials science,chemical engineering, biology

7 Shift of research paradigm • 1998 Nobel Prize in Chemistry with one half to Professor JOHN A. POPLE • Pople has developed quantum chemistry into a tool that can be used by the general chemist and has thereby brought chemistry into a new era where experiment and theory can work together in the exploration of the properties of molecular systems. Chemistry is no longer a purely experimental science. • In other words, theory/computation/simulation has become experiment in silico; • Not only for chemistry: physics, materials science, chemical engineering, biology

Nobelprizesfortheoretical/computationalchemistryRobertS.Mulliken1966"for his fundamental work concerning chemical bondsand the electronic structure of molecules by themolecular orbital method"Kenichi Fukui and Roald Hoffmann 1981"for their theories, concerning the course of chemicalreactions"Walter Kohn and John Pople 1998"for their developments of density-functional theory andcomputationalmethodsinquantumchemistryMartin Karplus, Michael Levitt, and Arieh Warshel 2013"for the development of multiscale models for complexchemical systems"8

8 Nobel prizes for theoretical/computational chemistry • Robert S. Mulliken 1966 “for his fundamental work concerning chemical bonds and the electronic structure of molecules by the molecular orbital method” • Kenichi Fukui and Roald Hoffmann 1981 “for their theories, concerning the course of chemical reactions” • Walter Kohn and John Pople 1998 “for their developments of density-functional theory and computational methods in quantum chemistry” • Martin Karplus, Michael Levitt, and Arieh Warshel 2013 “for the development of multiscale models for complex chemical systems

Anexemplarydisputeofmodels1.low barrier hydrogen bondW.WallaceCleland(Wisconsin-Madison,oldopponentdied2013),PerryA.Frey(Wisconsin-Madison),JohnAGerlt(UIUC)ChristopherJ.Halkides(NorthCarolinaWilmington)Christopher J.Murray (U ofWashington),OnCatalyticPreorganization inMildvan,A.S.(Johns Hopkins)Oxyanion Holes: Highlighting theKimKS(PohangUniversityofScienceandTechnology)BruiceTC (UCat Santa Barbara)Problems with the Gas-Phase Modeling2.minimal gas phase modelsof Oxyanion Holes and IllustratingtheMichaelA.McAllister (University of North Texas, Denton)Herschlag,D.(Stanford)NeedforCompleteEnzymeModels3.reactantstatedestabilizationShina C.L.Kamerlin,Zhen T.Chu,and A.WarshelGoodman，J.M（Cambridge，重点批判对象）Broadwith,P (Science correspondent)J. Org. Chem. 2010, 75, 6391-6401GaoJ(Wisconsin-Madison)MoY(WesternMichiganU)TinaL.Amyes (SUNYBuffalo)[lackof"logicalanalysis")Jencks,W.P(died2007,NationalAcademyofSciencesin1971)4.simplifiedtheozymemodelHoukKN(UCLA),BakerD (U ofWashington),Stoddard, B. L.(UCLA);5."contradictions of the first law of thermodynamics"GaoJ(Wisconsin-Madison)Truhlar,D.G(Wisconsin-Madison)9

1. low barrier hydrogen bond W. Wallace Cleland (Wisconsin-Madison, old opponent died 2013), Perry A. Frey(Wisconsin-Madison), John A Gerlt (UIUC), Christopher J. Halkides (North Carolina Wilmington), Christopher J. Murray (U of Washington), Mildvan, A. S. (Johns Hopkins) , Kim KS (Pohang University of Science and Technology), Bruice TC (UC at Santa Barbara) 2. minimal gas phase models Michael A. McAllister (University of North Texas, Denton) Herschlag, D. (Stanford) 3. reactant state destabilization Goodman, J. M (Cambridge，重点批判对象) Broadwith, P (Science correspondent) Gao J (Wisconsin-Madison) Mo Y (Western Michigan U) Tina L. Amyes (SUNY Buffalo) [lack of " logical analysis"] Jencks, W. P (died 2007, National Academy of Sciences in 1971) 4. simplified theozyme model Houk KN (UCLA), Baker D (U of Washington), Stoddard, B. L.(UCLA); 5. "contradictions of the first law of thermodynamics" Gao J (Wisconsin-Madison) Truhlar, D. G (Wisconsin-Madison) 9 An exemplary dispute of models On Catalytic Preorganization in Oxyanion Holes: Highlighting the Problems with the Gas-Phase Modeling of Oxyanion Holes and Illustrating the Need for Complete Enzyme Models Shina C. L. Kamerlin, Zhen T. Chu, and A. Warshel J. Org. Chem. 2010, 75, 6391–6401

Simulation(modeling/computation/theory)andexperimentCaondu"I'msearchingformykeys."Becausethe light here is so much better!10

Simulation (modeling/computation/theory) and experiment 10 Because the light here is so much better!

ModelIf I'd kuowm Hhey Wanfed metouseallisinfo-Model: Anencapsulated"black- wouidneverhaveasked forit!box"can predict properties.Given necessary input, itautomaticallyprovides relevantoutput;Build a model:: Simplification is the key;Use a model:.Information lost inevitable;Attitude: principles (the more the Must find descriptors;better)and limitations (must know);.Mechanismfor automation:. Levels of modeling: a) take-then-use,input-> output (qualitativeb)minor adjustments, c)majorand quantitative);modification, d) build new models:.Understand your model & system:·Able to predict: direction ofmisuse & abusing modelssystems'evolution11

Model 11 Model：An encapsulated ”black￾box” can predict properties. Given necessary input, it automatically provides relevant output; Build a model: • Simplification is the key; • Information lost inevitable; • Must find descriptors; • Mechanism for automation: input-> output (qualitative and quantitative); • Able to predict: direction of systems’ evolution • Attitude: principles (the more the better) and limitations (must know); • Levels of modeling: a) take-then-use, b)minor adjustments, c) major modification, d) build new models: • Understand your model & system: misuse & abusing models Use a model: