Accurate 3D Modeling of User Inputted Molecules Computer Systems Lab: 2007-2008 Ben Parr Period 6.

Slides:

Advertisements

Similar presentations

1 Molecular Geometry and VSEPR Theory Chapter 4 Pages Mrs. Weston Advanced Chemistry.

Advertisements

Molecular Geometry and Polarity

Computational Chemistry – Does WebMO enhance student learning? Brett Block Paris High School.

Molecular Geometry Lewis structures show the number and type of bonds between atoms in a molecule. –All atoms are drawn in the same plane (the paper).

Molecular shapes Balls and sticks. Learning objectives  Apply VSEPR to predict electronic geometry and shapes of simple molecules.

Correlated ab Initio Methods. Goal: select the most accurate calculation that is computationally feasible for a given molecular system Model chemistry:

Drawing Lewis Structures Hydrogens are always on the outside.

Chapter 10. VSEPR - Lewis structures do not help us predict the shape or geometry of molecules; only what atoms and bonds are involved. To predict shape.

Properties of Bonds Polarity Bond Order Bond Length Bond Energy.

Chapter 8 Second set of Chapt. 8 homework dates extended until after break Lab Notes Today’s Topic: Electron Distribution in Molecules (8.5) Molecular.

MO Diagrams for Diatomic Molecules Chapter 5 Friday, October 17, 2014.

(1) Covalent bonding: sharing of electron pairs by atoms

Chemistry 101 : Chap. 9 Molecular Geometry and Bonding Theories (1) Molecular Shape (2) The VSEPR Model (3) Molecular Shape and Molecular Polarity (4)

Chapter 3: Molecular Shape and Structure

Molecular Structure VSEPR Model. VSEPR Valence Shell Electron Pair Repulsion The structure around a given atom is determined principally by minimizing.

VSEPR Model And Hybridization. VSEPR Model Valence Shell Electron Pair Repulsion Model a simple model that allows for the prediction of the approximate.

Molecular Polarity & Intermolecular Forces

C HAPTER 9: M OLECULAR GEOMETRY AND BONDS. J ANUARY 28 TH, 2013 Do Now: Calculate the ∆H: C 2 H 4 + HCN  CH 3 CH 2 CN.

AP Chapter 9 Molecular Geometry and Bonding Theories HW:

Regression Lines. Today’s Aim: To learn the method for calculating the most accurate Line of Best Fit for a set of data.

Chapter 8 Molecular Shape The shape of a molecule can be important in determining its chemical reactions Molecular shape is often very important in the.

Chemical Bonding II: Molecular Geometry and Hybridization of Atomic Orbitals Chapter 10 Copyright © The McGraw-Hill Companies, Inc. Permission required.

Molecular Geometry Chemistry Mrs. Deiseroth. Molecular Geometry the 3-D arrangement of a molecule’s atoms in space the polarity of each bond, along with.

Dipole Moments and Polar Molecules 10.2 H F electron rich region electron poor region    = Q x r Q is the charge r is the distance between charges.

Intermolecular Forces. Intermolecular forces The attraction and repulsion forces between molecules – (intramolecular forces are the forces within the.

Valence Bond & hybridization

Section 12.1 Characteristics of Chemical Bonds 1.To learn about ionic and covalent bonds and explain how they are formed 2.To learn about the polar covalent.

Chemistry XXI Unit 2 How do we determine structure? M4. Inferring Charge Distribution Analyzing the distribution of electrons in molecules. M3. Predicting.

Developing a Force Field Molecular Mechanics. Experimental One Dimensional PES Quantum mechanics tells us that vibrational energy levels are quantized,

Co-processors for speeding up drug design algorithms Advait Jain Priyanka Jindal Pulkit Gambhir Under the guidance of: Prof. M Balakrishnan Prof. Kolin.

EXAMINING POLARITY. MICRO-TO-MACRO We have studied the shapes and structures of molecules The shape of a molecule affects how that molecule behaves The.

Accurate 3D Modeling of User Inputted Molecules Using a Hill- Climbing Algorithm Ben Parr Period 6.

Intermolecular Forces May the Force be with you, Or not??

1 Mr. ShieldsRegents Chemistry U10 L04 2 Molecular Shapes When considering molecular shapes three things must be considered: 1) What kind of bonds are.

 Basic Terminology  Molecule  Group of atoms held together by covalent bonds  Bond Length  Distance between 2 bonded atoms  Bond Energy  Energy.

 Basic Terminology  Molecule  Group of atoms held together by covalent bonds  Bond Length  Distance between 2 bonded atoms  Bond Energy  Energy.

Chapter 9 Molecular Geometries and Bonding Theories

What do all these images have in common?. The 4 images all contain “dipoles”, or two poles. BBBBattery: + and – ends MMMMagnet: two opposite ends.

Accurate 3D Modeling of User Inputted Molecules Using a Nelder Mead Algorithm Ben Parr Period 6.

Chemical Bonding II: VESPR

Chemistry 141 Monday, November 6, 2017 Lecture 26

Chemical Bonding II: Molecular Geometry and Hybridization of Atomic Orbitals Chapter 10 Copyright © The McGraw-Hill Companies, Inc. Permission required.

CHEMISTRY Matter and Change

Sections 9.4 & 9.5 Molecular Geometries and Bonding Theories

Write the word and the letter of the corresponding definition

7.10 – NOTES Shapes for Covalent Structures

Chemistry 141 Friday, November 10, 2017 Lecture 28 Bond Enthalpy

Fall 2015 Exam III 1. c 9. b 16. (next slides)

Valence Shell Electron Pair

MOLECULAR GEOMETRY Topic # 18

Valence Shell Electron Pair Repulsion Theory (VSEPR)

Chemistry 141 Wednesday, November 8, 2017 Lecture 27

Chapter 6 – 3 Molecular Geometry (p. 214 – 218)

Molecular Shapes and Hybrid Orbitals

Computational Chemistry – Does WebMO enhance student learning?

7.7 – NOTES Shapes for Covalent Structures

Valence Shell Electron Pair Repulsion Theory

Polar Molecules Link to Phet Polar Molecules.

Section 8.3 Bond Properties

Molecular shapes.

Electron Pair Geometries vs. Shape

10.5 (exceptions) Tro's Introductory Chemistry, Chapter 10.

Molecular Shapes VSEPR Model

Molecular Geometry and Polarity

The SHAPES of molecules

Molecular Shapes In order to predict molecular shape, we assume the valence electrons repel each other. Therefore, the molecule adopts whichever 3D geometry.

N19 - VSEPR and the 3D Geometry of Molecules

Chemical Bonds (Covalent Models)

Presentation transcript:

Accurate 3D Modeling of User Inputted Molecules Computer Systems Lab: Ben Parr Period 6

Goal Create program to let users easily and intuitively create simple molecules  Water (H 2 O)‏  Benzene (C 6 H 6 )‏  Nicotine (C 10 H 14 N 2 )‏ Have the program position the atoms correctly Easy viewing for a better understanding of the geometry of molecules

Background Understanding the geometry of molecules is extremely helpful Buying molecule modeling sets for every student in an introductory chemistry is too costly Some software similar to my project is also costly No real feasible option for beginner chemistry students

Nelder Mead Algorithm Used to “Auto-Position Atoms” Uses a simplex with N+1 vertices  N = 3*number of atoms  Each vertex represents a model Minimizes an energy function Ends when it reaches a tolerance

Energy Function Calculates energy of a vertex of the simplex (model)‏ 3 factors affect energy  Distance between every non-bonded pair of atoms (maximize)‏  Distance between bonded atoms (get as close to defined value)‏  Bond angles (maximize)‏ Does not take polarity into account

Current State All graphics and user interface implemented and work correctly All components of the Nelder Mead Algorithm are programmed  Energy function  Original simplex  Actual algorithm Very simple molecules position correctly Larger the molecule, the more incorrect the auto- positioning

Auto-Positioning for CO 2

Auto-Positioning for Propyne: C 3 H 4

Auto-Positioning of Benzene: C 6 H 6

If I had More Time... Create a better original simplex  Currently using mostly random numbers  Works, but could be changed to better suit the problem Account for polarity  Lone pair electrons  Current program won’t position atoms of water (H 2 O) correctly Refine Nelder Mead algorithm to work better for larger molecules