Slide 1

CEM 888: Molecular Modeling: Applications for Experimentalists What can theory do for the practicing chemist? What do we wish it could do? A brief progress report with examples on the performance and practical utility of theoretical tools for non-theoreticians

Slide 2

The Evolving Roles of Theory Pattern-matching>Explanatory> Exploratory>Predictive>Prescriptive? Organize data around common themes Develop physical insights into data Interpolate and extrapolate from data to analogous systems Predict results for proposed new expts Identify and propose new experiments

Slide 3

Wish List (add items as desired) Zeroth order wishes: Theory should always get the answer right Should be applicable to real molecules, materials, and situations Should teach us something so we can better think about science (who wants to always need a supercomputer in their back pocket?)

Slide 4

Chemistry Wishes: Structure Internal: distances, angles, dihedrals Rotational constants and symmetry Conformational preferences Solvation sphere Lattice packing Sensitivity to environment (solvent, pressure, fields, etc.)

Slide 5

Chemistry Wishes: Energetics Heats of formation Isomer relative energies Effect energies: strain, aromaticity, solvation, etc. Heats of fusion, vaporization; heat capacities Ionization potentials/e affinities UPS/XPS, E-chem, redox reagent chemistry Bond strengths, atomization energies MS, reaction paths

Slide 6

Chemistry Wishes: Observables Melting and boiling points Density, viscosity Refractive index, optical rotation, CD/ORD Solubilities in various solvents pK a (or other ionic dissociation abilities) Dipole, polarizability Magnetic susceptibility and e -e coupling

Slide 7

Chemistry Wishes: Spectroscopies UV-vis-IR/Raman-wave absorption/emission Peak positions Transition intensities, rates (Abs, ISC, Emission, Internal conv.) NMR Chemical shifts, Spin-spin couplings, J AB Relaxation times NOE intensities Conformational dynamics EPR Spin densities Hyperfine coupling constants

Slide 8

Chemistry Wishes: Reactivity and Mechanism Activation parameters Transition state structures and reaction paths Conformational interconversion barriers (NMR) Isotope effects Solvent effects on all (structure, energetics, etc.)

Slide 9

Chemistry Wishes: New Insights Charge allocation to atoms--meaningful? Why arent some classically valid-looking structures stable? Are orbitals or resonance structures real? How about ring currents Steric vs. Electronic effects VSEPR?

Slide 10

Performance of the Methods: Structure Ordinary compounds--simple hydrides AH n LiH, BeH 2, BH 3, BH 4 , CH 4, NH 3, NH 4 +, OH 2, FH NaH, MgH 2, AlH 3, AlH 4 , SiH 4, PH 3, PH 4 +, SH 2, ClH Simple A-B bonded systems H m A-BH n H 3 C-CH 3, H 2 N-NH 2, HO-OH, F-F H 3 C-NH 2, H 3 C-OH, H 3 C-F, etc. Multiple bonded AB systems ABH n

Slide 11

Beyond Minima: Reactions Potential Energy Surfaces Transition Structures Reaction Paths Transition States Reaction Rates

Slide 12

Generic Textbook Reaction Path Usually for unimolecular processes How are stationary points and reaction path defined? Are they unique and independent of coordinate system? What is a Reaction Coordinate anyway, in 3n-6 dimensions?

Slide 13

Simplest P.E. Curve: Diatomics Diatomic dissociation is familiar Linear structure: 3n-5 =1 mode Reaction Coord. is uniquely defined as r(AB)

Slide 14

Generic Reaction Path Common for bimolecular processes In gas phase, two fragments always stick together a bit. TS may be above or below fragment totals. Minima may have inverse E order e.g. H 3 O

Slide 15

Rxn Paths: TS Vibrational Modes From Anwar G. Baboul and H. Bernhard Schlegel, Improved method for calculating projected frequencies along a reaction path J. Chem. Phys. 1997, 107, 9413-9417. Vibrations in the TS for the (degenerate) S N 2 attack of Cl on CH 3 Cl. Note: all but the Reaction Coord motion are positive ordinary vibrations

Slide 16

The Transition Structure Stationary Point (i.e. gradients ~ 0) One imaginary frequency (Nimag=1) Locate by minimizing gradient ( E/ x i ) Structure is independent of coordinate system, nuclear masses Is this structure the transition state? How to get close enough for local optimizn

Slide 17

Searching for the MEP or IRC At the TS only, the reaction coord is well defined, as the mode with the imaginary freq. From TS, follow steepest descent at each step. Reaction path points not independently defined; path curves (i.e. rxn coord makeup varies) Search scheme, step size, intermediate optimization are all important.

Slide 18

Sample PES

Slide 19

Anglada, J. M.; Besal, E.; Bofill, J. M.; Crehuet, R. J. Comput. Chem. 2001, 22, 387-406. Figure 9. The Mller- Brown potential surface. Dashed line, energy contours. Solid line is the reduced potential surface defined as g x 0, g y =0. The black circles are the stationary points, minimum, M1 and M2, transition state, TS1. The empty circles are the starting point, P, and the turning point, TP. The black dots are the different points evaluated by the algorithm; see text for more details.