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Gary DeBoer Associate Professor of Chemistry LeTourneau University Oct. 4, 2007 11:00 am, C101

Gary DeBoer Associate Professor of Chemistry LeTourneau University Oct. 4, 2007 11:00 am, C101. Modeling summer fashions in chemistry: The far out, radical behavior of the O atom. Dumb. Modeling surfaces, Can tell us things, like about life on Mars. April 6, 1998 Viking. 10.4.

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Gary DeBoer Associate Professor of Chemistry LeTourneau University Oct. 4, 2007 11:00 am, C101

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  1. Gary DeBoer Associate Professor of Chemistry LeTourneau University Oct. 4, 2007 11:00 am, C101 Modeling summer fashions in chemistry: The far out, radical behavior of the O atom

  2. Dumb

  3. Modeling surfaces, Can tell us things, like about life on Mars April 6, 1998 Viking

  4. 10.4 Energy = function (distance between atoms)

  5. E = F(q1,q2)

  6. Q. How do we model the shape of our surface?A. We use computational chemistry software.Q. Which?A. GaussianQ. What does the software do?A. It calculates the solution to the Shrodinger Equation. HY = EY

  7. Types of Modeling • Energies and geometries • Molecular mechanics • Semi-empirical • Ab initio • i. Hartree-Fock (HF) • ii. Perturbation methods (MP2) iii. Density Functional Theory (DFT) • iv. Compound methods, G3, CBS-QB3 • Kinetics • RRKM using Multiwell • Ab intio/Molecular Dynamics • NWChem/Venus

  8. The call of the O atom…

  9. O + NO a NO2* Q. Why in the world oxygen atom chemistry? A. My chemistry is not of this world. Chang, General Chemistry http://www.vs.afrl.af.mil/Gallery/ http://jan.ucc.nau.edu/doetqp/courses/env440/env440_2/lectures/lec32/lec32.htm

  10. What we want to model? • O(3P) + HCO • addition to O • abstraction of H • addition to C Atoms and small molecules are best addressed from an ab initio perspective

  11. ********************************************** Gaussian 03: x86-Win32-G03RevB.02 16-Apr-2003 25-Jun-2007 ********************************************** %chk=06-25-07 18 Default route: Opt=MaxCyc=200 QCISD=Maxcyc=200 MaxDisk=32GB ------------------------------------- # freq uhf/6-31g(d) geom=connectivity ------------------------------------- 1/6=200,10=4,30=1,38=1,57=2/1,3; 2/17=6,18=5,40=1/2; 3/5=1,6=6,7=1,11=2,16=1,25=1,30=1/1,2,3; 4/7=2/1; 5/5=2,38=5/2; 8/6=4,10=90,11=11/1; 10/13=10/2; 11/6=2,8=1,9=11,15=111,16=1/1,2,10; 10/6=1/2; 6/7=2,8=2,9=2,10=2,18=1,28=1/1; 7/8=1,10=1,25=1/1,2,3,16; 1/6=200,10=4,30=1/3; 99//99; -------------------------------- 06-05-07 02 #15 uHF 6-31(d) freq -------------------------------- Symbolic Z-matrix: Charge = 0 Multiplicity = 2 C H 1 B1 O 1 B2 2 A1 O 1 B3 3 A2 2 D1 0 Variables: B1 1.10999 B2 1.15946 B3 2.75115 A1 131.36645 A2 126.41384 D1 180. GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Berny optimization. Initialization pass. ---------------------------- ! Initial Parameters ! ! (Angstroms and Degrees) ! ---------------------- ---------------------- ! Name Value Derivative information (Atomic Units) ! ------------------------------------------------------------------------ ! B1 1.11 calculate D2E/DX2 analytically ! ! B2 1.1595 calculate D2E/DX2 analytically ! ! B3 2.7512 calculate D2E/DX2 analytically ! ! A1 131.3664 calculate D2E/DX2 analytically ! ! A2 126.4138 calculate D2E/DX2 analytically ! ! D1 180.0 calculate D2E/DX2 analytically ! ------------------------------------------------------------------------ Trust Radius=3.00D-01 FncErr=1.00D-07 GrdErr=1.00D-07 Number of steps in this run= 2 maximum allowed number of steps= 2. GradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGradGrad Input orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 6 0 0.000000 0.000000 0.000000 2 1 0 0.000000 0.000000 1.109986 3 8 0 0.870173 0.000000 -0.766255 4 8 0 -2.688818 0.000000 -0.582311 --------------------------------------------------------------------- Distance matrix (angstroms): 1 2 3 4 1 C 0.000000 2 H 1.109986 0.000000 3 O 1.159460 2.068207 0.000000 4 O 2.751151 3.177045 3.563742 0.000000 Stoichiometry CHO2(2) Framework group CS[SG(CHO2)] Deg. of freedom 5 Full point group CS NOp 2 Largest Abelian subgroup CS NOp 2 Largest concise Abelian subgroup C1 NOp 1 Want to model the chemistry to explain and predict experimental work.

  12. Overview • Introduce the ab initio methods • Report on current ab initio results • Present future goals for molecular dynamics • Highlight and review Yarnell Hill, a curvy stretch of Arizona highway.

  13. Douglas HartreeSelf Consistent Field method for finding Y, and then E. (1928) • Assumes that Y is a product of one electron, Y(n)’s, initially guessed, Y0 . • The individual Y0(n)’s are each optimized by letting each of the n electrons pass through a field produced by an average influence of all the remaining electrons. After each Y0(n)’s is optimized once, we produce Y1. • This process is repeated again and again until the resulting energy no longer changes and we have converged upon the best Y, Yk. • In 1930, Fock and Slater, corrected the Hartree method for spin, thus creating the Hartree-Fock Self Consistent Field, or HF-SCF, method. • Computational solutions are found using methods of linear algebra. The HF-SCF method produces an error called electron correlation

  14. Edward Teller Niels Bohr Otto Frisch Fritz Kalckar Milton Plesset Fixing the electron correlation problem Approach 1. Moller-Plesset (MP) Theory, 1934, the pure, but slower route. The E2 term comes from a new H’Y = E2Y in which ‘virtual orbitals’ are made available for electrons to enter. The result is, less crowded, happier electrons, at lower energy. Came to practical development in 1975, by Pople. The MP2 and MP4 methods require lots of integrals for all the differing components of Ya slow. 1938 or earlier

  15. Fixing the electron correlation problem r*external k.e. of electrostatic exchange potential + electrons + repulsion + correlation functional Approach 2, Density Functional Theory, DFT, the less than pure, somewhat semi-empirical, but faster route. Fermi and Dirac, 1920’s to Parr and Yang, 1989 Decreases all the variables of Y to only three: x,y, and z. Exc is determined empirically

  16. B3LYP functionalBecke 3 Lee-Yang-Parr These parameters are adjustable and Song reports having adjusted them to fit the DFT/B3LYP/6-31G(d) results to higher level calculations for his OH + CO work. These optimized parameters for the OH + CO reaction should also be valid for our O + HCO reaction. Accurate and fast DFT/B3LYP/6-31G(d) calculation should benefit our MD/QM calculations using Venus/NWChem.

  17. ‘s are linear combinations of atomic orbitals LCAO’s, each AO being modeled with basis sets STO-3G 1 Atomic Orbital = 1 Slater Type Orbital = 3 Gaussians. 1 contracted function = 3 primitives Gaussians. An example of a minimal basis set 1 atomic orbital = 1 contracted function (STO-3G) Eg. Carbon, element 6, would be modeled with 1s, 2s, and 3 2p’s atomic orbitals, 5 contracted STO-3G’s 15 primitive Gaussians.

  18. 6-31G(d) or 6-31G* A split valence basis set with polarization. The core oribitals are described with 1 contracted function composed of 6 primitive Gaussian functions The valence orbitals are split into inner and outer shells. The inner valence shell 1 contracted function = 3 primitive Gaussian functions. The outer valence shell 1 contracted function = 1 primitive Gaussian function. Eg. Carbon, element 6, 1s, 2s, 2s’, 3 2p, and 3 2p’ atomic orbitals = 9 contracted functions, 6 +(3 + 1) + 3*(3 + 1)=22 primitive Gaussians. The (d) or the * denotes that polarization has been added. This adds 6 d orbitals (1 primitive gaussian) to the previous 9 contracted basis functions for a total of 15 contracted basis functions or 28 primitives . C, 2 O’s, H, would give 3*15 + 2 (1s +1s’), hydrogen doesn’t get a d) = 47 contracted functions, or 88 primitive Gaussians.

  19. Fixing other problems like polarization, diffusion, and so on through compound methods • G3 • HF/6-31G(d) geometry optimization and frequency • MP2(full)/6-31G(d) geometry optimization • QCISD(T,E4T) 6-31G(d)energy • MP4/6-31G+(d) • MP4/6-31G(2df,p) • MP2(full)/GTlarge • Empirical spin correction • CBS-QB3 complete basis set • DFT/B3LYP/CBSB7 geometry optimization and frequency • CCISD(T)/6-31+G(d) energy • MP4SDQ/CBSB4 energy • MP2/CBSB3 energy • CCSD(T) energy • Empirical spin correction Both methods estimate polarization, diffusion, and other such things by comparing outcomes from the different steps. Small basis set calculations can then predict the larger basis set results.

  20. These numbers allow us to build our potential energy surface

  21. Some illustrative examples TS6 IRC TS8 IRC TS1a IRC

  22. k = A exp(-Ea/RT)

  23. Spencer Falls Greensville, Ontario

  24. Niagara Falls, NY

  25. Smart E = mc2 PV=nRT Brooke Shields after having taken general chemistry at LeTourneau University

  26. Smart Modeling of Kinetics RRK Rice, Ramsperger, and Kassel, 1927 RRKM = RRK + modification to correct for zero point energy (ZPE) Sum of states for the transition species Density of states of reactants

  27. Transition State Products Reactants

  28. How to resolve these uncertainties in weightings? Molecular Dynamics – future work • start with molecules in a randomly oriented system, with a given distribution of energies. • let them fly, a bit, • calculate energies and determine the vectors of the forces • follow those vectors, a bit, • return to 3, until one reaches a minimum HeH2+ LEPS Potential NH2OH a NH2 + OH NH2OH a NH3 + O

  29. Q. DeBoer, why should my tax dollars go to support your summer fun? • Space Asset and Missile Defense? B. Basic research C. Long term security D. Build collaborative research relationships for LeTourneau students E. You too, can be a space scholar

  30. What should we take home? • Models can be used to explain and predict the chemistry of the O atom. • Want the models to be fast and accurate. • Are you a model student?

  31. Integration Intuition aided by experience and reason Reason, logic, systems of thought to reach assurance of knowledge Theories of Philosophy/theology that explain observations of the human condition Theories of natural science that explain the observed behavior of matter and biological systems

  32. Watch the PBS special on evolution and God EVOLUTION Features Ken Ham and Wheaton College Bill Hansen Steve Ball Karen Rispin Glaske C101 Friday Oct. 5 7:00 pm Bible Physics Biology If true, what then of Creation? Discuss after with LU faculty Fall? Redemption? A Socratic Forum – Sci Phi Event

  33. Acknowledgement Jim Dodd Jennifer Gardner US Air Force Office of Sponsored Programs USAFRL Summer Faculty Fellowship Program ASEE Welch Foundation

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