this is the work on PES done by me referencing all available molecular modelling books And it also contains Molecular graphics as its second part

1. POTENTIAL ENERGY SURFACE (PES) MOLECULAR GRAPHICS Presentation By S.Prasanth Kumar

2. POTENTIAL ENERGY SURFACE (PES)

5. H ψ = E ψ For a general quantum system Describes how the quantum state of a physical system changes in time Schrödinger equation i imaginary unit Ψ(r, t ) wave function ħ Planck constant Hamiltonian operator

6. Also considers Electronic Energy Of Each Of These Orientations

7. A potential energy surface must be created to take into account : 1.Every possible orientation of the reactant molecules 2.Every possible orientation of the product molecules 3.The electronic energy of the reactant molecules 4.The electronic energy of the product molecules

9. The time-independent Schrödinger equation In the Born-Oppenheimer approximation the wave function is written as a product function ψ E (r, σ ,R) ψ B.O = ψ e (r, σ ;R) Φ (R)

10. Equation for electronic motion: Remember: r Electronic Coordinates R Nuclear Coordinates The Potential Energy Surface (PES) depends parametrically on the position of the nuclei R

11. The electronic wavefunction is a solution of the electronic Schrödinger equation The Schrödinger equation for the nuclear wave function

12. Transition state The state corresponding to the highest energy along the reaction coordinate Reaction Coordinate Coordinate of a geometric parameter that changes during the conversion of one or more molecular entities bond length, bond angle , bond order, . . . . . . . . . .

13. LOCAL MINIMA LOCAL MAXIMA Ethane Dihedral Motion

14. CH 2 Cl-CH 2 Cl Dihedral Motion GLOBAL MINIMUM

15. Saddle Points {Minimum in all variables except one variable, Maximum in this Excepted variable} Saddle Point 2 minima & a Saddle point This corresponds to a transition state in theories of reaction mechanisms

16. Minima, Maxima & Saddle Points

17. COURTESY : Molecular Modeling:Geometry Optimization-Introduction to Cheminformatics II by Kelsey Forsythe Cyclohexane

18. The Real Picture….

19. What these points tell us ? Global Minimum Energy value corresponds to the most stable nuclear configuration Reaction Coordinate The path along the potential energy surface that the atoms "travel" during the chemical reaction Saddle Points or Correspond to transition Local Maxima states Local Minima Reactive Intermediates

20. It’s the Right time to define the Potential Energy Surface. . . . A geometric hyper surface on which the potential energy of a set of reactants is plotted as a function of the coordinates representing the molecular geometries of the system

21. A PES displays the energy of a molecule as a function of its geometry Potential Energy Geometric Coordinate e.g. bond length Potential Energy Geometric Coordinate s e.g. bond length, bond order 1-D 3-D

23. APPLICATIONS

27. MOLECULAR GRAPHICS : The discipline and philosophy of studying molecules and their properties through graphical representations

28. MILESTONES Early Cathode ray tube screens or through plotters drawing on paper 1966 Display of a protein molecule (Project MAC) - Cyrus Levinthal and Robert Langridge Realistic" Rendering Of Macromolecules Using Reflecting Spheres - Nelson Max 1982 Molecular Graphics Society (MGS) in UK 1980s Programs for calculating molecular properties (such as molecular dynamics and quantum mechanics) Molecular Graphics and Modelling Society (MGMS)

30. 3-D Rendered Image x,y,z coordinates should be known All geometric transformations (rotation, scaling, etc) can be done

32. Ambient occlusion Ambient occlusion is a global lighting technique Concept : light each point p with normal vector with its computed irradiance. Irradiance : the quantity of light reaching p from any direction… Local lighting Ambient Occlusion

33. Ambient occlusion applied to Proteins WITHOUT AMBIENT OCCLUSION WITH AMBIENT OCCLUSION

34. DIFFERENT ATTRRIBUTES TRANSLATION :A translation moves an object into a different position in a scene SCALING : A scaling changes the size of an object with two scale factors, Sx and Sy

35. ROTATION : Using the trigonometric relations, a point rotated by an angle about the origin SHEARING : A shearing affects an object in a particular direction (in 2D, it’s either in the x or in the y direction)

36. DIFFERENT MODELS USED IN VISUALIZATION SOFTWARES

37. Ribbon Model Structure of Hemagglutinin Ligand: Sialic Acid Alpha Helices Carbon Oxygen Nitrogen

38. Space-Fill Models Structure of Formic Acid Atoms are drawn to suggest the amount of space they occupy CPK Model = Corey, Pauling, Koltan The quantum mechanical representation of molecules, there are only (positively charged) nuclei and a "cloud" of negative electrons. The electron cloud defines an approximate size for the molecule

39. Isosurface Zirconocene where part (left) is rendered as ball-and-stick and part (right) as an isosurface. Isosurfaces that have been coloured to show quantities such as electrostatic potential Negative Positive Neutral

40. Stick Model Space-Fill Model

41. Cylindrical or "Licorice" modes Cylindrical-Med

42. But Not the least, The Animation

43. RasMol Swiss PDB viewer Molscript Ribbons Grasp VMD WebMol Chime Cn3D PyMol QMol Structure Visualization & Manipulation Softwares

44. References: POTENTIAL ENERGY SURFACE (PES) Molecular Modelling : Principles and Applications by Andrew R Leech Molecular Modelling for Beginners by Alan Hinchliffe, UMIST, Manchester, UK Potential energy surfaces and applications for CmHn by Bastiaan J. Braams Emory University with Joel M. Bowman MOLECULAR GRAPHICS (MG) History of Visualization of Biological Macromolecules by Eric Martz and Eric Francoeur. Brief History of Molecular Mechanics/Graphics in LSU CHEM7770 lecture notes Desktop Molecular Modeling by Peter L.Hurray Ambient Occlusion and Edge Cueing for e nhancing Real Time Molecular Visualization by Marco Tarini, Paolo Cignoni, Claudio Montani Online Programs: PDB, JMol,

45. FOR YOUR ATTENTION