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 ”blackbox” 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: