1 Introduction to Computational Chemistry (Spartan)
|
|
|
- Winfred Campbell
- 6 years ago
- Views:
Transcription
1 1 Introduction to Computational Chemistry (Spartan) Start Spartan by clicking Start / Programs / Spartan Then click File / New Exercise 1 Study of H-X-H Bond Angles (Suitable for general chemistry) Structure of CH 4 Using the Entry level builder, click on the sp 3 -hybridized C atom (first row, first column). Click in the workspace. The CH 4 skeleton appears. Click on the View icon (5 th across top). Rotate by left clicking and dragging. Rotate in the plane of the screen by Shift left clicking and dragging. Translate by right clicking and dragging. Zoom by Shift right clicking and dragging vertically. Click Submit. Save as ch4pm3.spartan in an appropriate folder. Click on the Distance icon (11 th across the top) and on a C-H bond. Record the C-H bond length (lower right corner of screen): Å (1.091Å lit.). Click on the Angle icon (12 th across top) and click on the H, C, H atoms (the order is important). Record the H-C-H bond angle: º ( º lit.). Structure of NH 3 Click New File (1 st icon at left at the top; paper with turned down corner). Click on the sp 3 -hybridized N atom (first row, second column). Click in the workspace. The NH 3 skeleton appears. Click Submit. Save as nh3pm3.spartan in an appropriate folder. Click on the Distance icon (11 th across the top) and on a N-H bond. Record the N-H bond length: Å (1.012Å lit.). Click on the Angle icon (12 th across top) and click on the H, N, H atoms (the order is important). Record the H-N-H bond angle º (106.67º lit.). Structure of H 2 O Click New File (1 st icon at left at the top; paper with turned down corner). Click on the sp 3 -hybridized O atom (second row, third column). Click in the workspace. The H 2 O skeleton appears.
2 Click Submit. Save as h2opm3.spartan in an appropriate folder. Click on the Distance icon (11 th across the top) and on an O-H bond. Record the O-H bond length: Å (0.959Å lit.). Click on the Angle icon (12 th across top) and click on the H, O, H atoms (the order is important). Record the H-O-H bond angle º (103.9º lit.). What conclusion(s) can you make concerning the H-X-H bond angle and the number of unshared (lone) pairs of electrons around the central atom X? Exercise 2 Study of the Rotation Barrier Energy about Carbon-Carbon Bonds (suitable for organic chemistry) Method A: Structure of Ethane, CH 3 CH 3 Using the Entry level, click on the sp 3 -hybridized C atom (first row, first column). Click in the workspace (the methane skeleton appears). Click again on the end of one of the yellow valences (the staggered ethane skeleton appears). Click on the view icon. Click Submit. Save as stagethanepm3.spartan in an appropriate folder. Click Display / Output. Scroll down and find the Heat of Formation towards the bottom. Record the value here kcal mol -1. Close the output window. Click New File Draw Ethane as instructed above, but DO NOT click the view icon. You should have a red rotation arrow on the C-C bond. Rotate (left click and drag) until you are looking down the C-C bond (Newman projection). Hold down the Alt key, place the cursor well away from the molecule, left click and drag until the completely eclipsed form of the molecule is produced. Rotate so the molecule is viewed side-on ( to the C-C bond). Click Constrain Dihedral (18 th across the top). Click on the atoms H-C-C-H so that the two H s are the ones which eclipse one another. With these four atoms highlighted, click on the lock icon in the lower right corner. (The numeric display should read 0.00º. If it does not, adjust it now and hit enter on the keyboard). Empirical PM3, Subject to Constraints. Click Submit. Save as eclipethanepm3.spartan in an appropriate folder. Click Display / Output. Scroll down and find the Heat of Formation towards the bottom. Record the value here kcal mol -1.
3 Close the output window. To calculate the barrier to rotation about the C-C bond, subtract the staggered value from the eclipsed value, and enter the result here kcal mol -1 (2.9 kcal mol -1 lit.). Method B: Structure of Ethane, CH 3 CH 3 Build a molecule of ethane as instructed above., and click on the View icon. Choose Geometry / Constrain Dihedral. Click on H, C, C, H atoms so that the two H s are anti (180º apart). Click on the pink unlocked icon in the lower right of the screen to lock it. (The numeric display in the lower right corner should read º). Choose Display / Properties. If needed, move the Selected style box from in front of the molecule. Zoom in on the molecule (Shift-Right click and drag vertically) and click on the pink constraint marker that appears on the midpoint of the C-C bond. Click the Dynamic box in the Constraint Properties window. Edit the second value box to 0.00º (YOU MUST HIT RETURN TO MAKE THIS CHANGE). The top line should read Value: º to 0.00º. Change Steps to 37 (YOU MUST HIT RETURN TO MAKE THIS CHANGE). Close the Constraint Properties box. Choose Setup / Calculations. Choose Energy profile at Ground State with Semi- Click Submit. Save as C2H6PM3.spartan in an appropriate folder. (The calculation takes several seconds). Choose File / Open / C2H6PM3.Profile1 Choose Display / Spreadsheet. Click on the Molecule001 cell to highlight it. Click on the gray box in Column 2, Row 1 (top box) to highlight it. Click Add / rel. E (relative energy). Click To add the angles to the spreadsheet, choose Geometry / Measure Dihedral. Click on the pink constraint marker on the C-C bond. Click on the yellow P box in the lower right of the screen. Choose Display / Plots. Choose X Axis / Dihedral(Con1) and Y Axes / rel. E (kcal/mol). Click To find the two angles where the energy is a minimum and a maximum, use the advance and reverse buttons on the bottom left. The corresponding angle and energy will be highlighted in the spreadsheet. Record the maximum energy: kcal mol -1 and minimum energy: kcal mol -1. To calculate the barrier to rotation about the C-C bond, subtract the maximum value from the minimum value, and enter the result here kcal mol -1 (2.9 kcal mol -1 lit.). Pressing the Play button (<) at the bottom of the screen will animate the bond rotation.
4 Structure of Ethene, C 2 H 4 Using the Entry level, build a molecule of ethene. Choose Geometry / Constrain Dihedral. Click on H, C, C, H atoms so that the two H s are trans (180º apart). Click on the pink unlocked icon in the lower right of the screen to lock it. Choose Display / Properties. If needed, move the Selected style box from in front of the molecule. Zoom in on the molecule (Shift-Right click and drag vertically) and click on the pink constraint marker that appears on the midpoint of the C=C bond. Click the Dynamic box in the Constraint Properties window. Edit the second value box to 0.00º (YOU MUST HIT RETURN TO MAKE THIS CHANGE). The top line should read Value: º to 0.00º. Change Steps to 37 (YOU MUST HIT RETURN TO MAKE THIS CHANGE). Close the Constraint Properties box. Choose Setup / Calculations. Choose Energy profile at Ground State with Semi- Click Submit. Save as C2H4PM3.spartan in an appropriate folder. (The calculation takes some time). Choose File / Open / C2H4PM3.Profile1 Choose Display / Spreadsheet. Click on the Molecule001 cell to highlight it. Click on the gray box in Column 2, Row 1 (top box) to highlight it. Click Add / rel. E (relative energy). Click To add the angles to the spreadsheet, choose Geometry / Measure Dihedral. Click on the pink constraint marker on the C=C bond. Click on the yellow P box in the lower right of the screen. Choose Display / Plots. Choose X Axis / Dihedral(Con1) and Y Axes / rel. E (kcal/mol). Click To find the two angles where the energy is a minimum and a maximum, use the advance and reverse buttons on the bottom left. The corresponding angle and energy will be highlighted in the spreadsheet. Record the maximum energy: kcal mol -1 and minimum energy: kcal mol -1. To calculate the barrier to rotation about the C=C bond, subtract the maximum value from the minimum value, and enter the result here kcal mol -1 (68 kcal mol -1 lit.). Pressing the Play button (<) at the bottom of the screen will animate the bond rotation. Exercise 3 Study of the Molecular Orbitals in Ethene, CH 2 CH 2 (suitable for physical chemistry) Click New File Click on the sp 2 -hybridized carbon atom (second row, first column).
5 Click in the workspace. Click again on the small sphere at the tip of the double bond. Empirical PM3, Print Orbitals and Energies. Click Submit. Save as ethenepm3.spartan in an appropriate folder. Choose Setup / Surfaces and Click Add. In the Add Surface Dialog box, choose Surface HOMO, Resolution Medium, then Click - Click Add again, choose Surface LUMO, Resolution Medium, then click (If desired, other MO s could be chosen by choosing HOMO-1, HOMO-2, LUMO+1, etc.). Close the Surfaces window. Click Setup / Submit. Choose Display / Surfaces and check the yellow box next to HOMO. If it is in front of the molecule, move (by dragging) the Surfaces window. Rotate the molecule to observe the π-orbital. In the Surfaces window, uncheck the yellow box next to HOMO, and check the yellow box next to LUMO. If needed, move the Surfaces window away from in front of the molecule. Rotate the molecule to observe the π*-orbital. Choose Setup / Surfaces and Click Add. In the Add Surface Dialog box, choose Surface Density, Property None, Resolution Medium, then Click Click Add, choose Surface Density, Property Potential, Resolution Medium, then click Click Add again, choose Surface Density (bond), Property None, Resolution Medium, then click Click Add again, choose Surface Density (bond), Property Potential, Resolution Medium, then click Close the Surfaces window. Click Setup / Submit. Click Display / Surfaces. The Surfaces window displays four densities, two of them with the property potential. The different numbers in the Isovalue column represent the electron density in units of electrons/au 3. Click in the yellow box to view the electron density at an isovalue of The volume roughly correlates to the common space filling view of molecules, and is an indication of molecular size (click on Model / Space Filling for comparison). Uncheck the first yellow box, and click the second one to view the electrostatic potential mapped onto the electron density. Red indicates (-) and blue indicates (+) charge. The other isovalue of electron density (0.08) shows a smaller surface (greater electron density), and better indicates the location of the bonding electrons. Save, Close, and exit the program.
5 Electron Densities, Electrostatic Potentials, and Reactivity Indices (Spartan)
5 Electron Densities, Electrostatic Potentials, and Reactivity Indices (Spartan) Exercise 1 Visualizing Different Bond Types Build the H 2 molecule. Save as dihydrogen.spartan in an appropriate folder.
Molecular Modeling and Conformational Analysis with PC Spartan
Molecular Modeling and Conformational Analysis with PC Spartan Introduction Molecular modeling can be done in a variety of ways, from using simple hand-held models to doing sophisticated calculations on
Introductory WebMO Exercises
Introductory WebMO Exercises These directions assume no prior knowledge of e WebMO interface and provide detailed, click by click instructions on building molecules and setting up calculations. Use your
Literature values: ΔH f, gas = % error Source: ΔH f, solid = % error. For comparison, your experimental value was ΔH f = phase:
1 Molecular Calculations Lab: Some guideline given at the bottom of page 3. 1. Use the semi-empirical AM1 method to calculate ΔH f for the compound you used in the heat of combustion experiment. Be sure
Learning to Use Scigress Wagner, Eugene P. (revised May 15, 2018)
Learning to Use Scigress Wagner, Eugene P. (revised May 15, 2018) Abstract Students are introduced to basic features of Scigress by building molecules and performing calculations on them using semi-empirical
Exercises for Windows
Exercises for Windows CAChe User Interface for Windows Select tool Application window Document window (workspace) Style bar Tool palette Select entire molecule Select Similar Group Select Atom tool Rotate
Chemistry 14CL. Worksheet for the Molecular Modeling Workshop. (Revised FULL Version 2012 J.W. Pang) (Modified A. A. Russell)
Chemistry 14CL Worksheet for the Molecular Modeling Workshop (Revised FULL Version 2012 J.W. Pang) (Modified A. A. Russell) Structure of the Molecular Modeling Assignment The molecular modeling assignment
Name. Chem Organic Chemistry II Laboratory Exercise Molecular Modeling Part 2
Name Chem 322 - Organic Chemistry II Laboratory Exercise Molecular Modeling Part 2 Click on Titan in the Start menu. When it boots, click on the right corner to make the window full-screen. icon in the
Introduction to Hartree-Fock calculations in Spartan
EE5 in 2008 Hannes Jónsson Introduction to Hartree-Fock calculations in Spartan In this exercise, you will get to use state of the art software for carrying out calculations of wavefunctions for molecues,
General Chemistry Lab Molecular Modeling
PURPOSE The objectives of this experiment are PROCEDURE General Chemistry Lab Molecular Modeling To learn how to use molecular modeling software, a commonly used tool in chemical research and industry.
Patrick: An Introduction to Medicinal Chemistry 5e MOLECULAR MODELLING EXERCISES CHAPTER 17
MOLECULAR MODELLING EXERCISES CHAPTER 17 Exercise 17.6 Conformational analysis of n-butane Introduction Figure 1 Butane Me Me In this exercise, we will consider the possible stable conformations of butane
Instructions for Using Spartan 14
Instructions for Using Spartan 14 Log in to the computer with your Colby ID and password. Click on the Spartan 14 icon in the dock at the bottom of your screen. I. Building Molecules Spartan has one main
Ethene. Introduction. The ethene molecule is planar (i.e. all the six atoms lie in the same plane) and has a high degree of symmetry:
FY1006 Innføring i kvantefysikk og TFY4215 Kjemisk fysikk og kvantemekanikk Spring 2012 Chemical Physics Exercise 1 To be delivered by Friday 27.04.12 Introduction Ethene. Ethylene, C 2 H 4, or ethene,
1 An Experimental and Computational Investigation of the Dehydration of 2-Butanol
1 An Experimental and Computational Investigation of the Dehydration of 2-Butanol Summary. 2-Butanol will be dehydrated to a mixture of 1-butene and cis- and trans-2-butene using the method described in
7 Infrared, Thermochemistry, UV-Vis, and NMR
7 Infrared, Thermochemistry, UV-Vis, and NMR Exercise 1 Method Dependence and Scaling for the Infrared Spectrum of Formaldehyde. Build a molecule of formaldehyde using sp 2 C and atoms. Clean up the structure
The Hückel Approximation Consider a conjugated molecule i.e. a molecule with alternating double and single bonds, as shown in Figure 1.
The Hückel Approximation In this exercise you will use a program called Hückel to look at the p molecular orbitals in conjugated molecules. The program calculates the energies and shapes of p (pi) molecular
Lewis Structures and Molecular Shapes
Lewis Structures and Molecular Shapes Rules for Writing Lewis Structures 1. Determine the correct skeleton structure (connectivity of atoms). Usually, the most electronegative atoms go around the edges
Assignment 2: Conformation Searching (50 points)
Chemistry 380.37 Fall 2015 Dr. Jean M. Standard September 16, 2015 Assignment 2: Conformation Searching (50 points) In this assignment, you will use the Spartan software package to investigate some conformation
Lewis Structures and Molecular Shapes
Lewis Structures and Molecular Shapes Rules for Writing Lewis Structures 1. Determine the correct skeleton structure (connectivity of atoms). Usually, the most electronegative atoms go around the edges
Contents. 1. Building a molecular model 2. Additional Procedures and Options: 3. Selecting a calculation method
Getting started with HyperChem. Program description. In this project you will create simple organic molecules and learn how to manipulate them. However, before starting you should create your home directory
Molecular Orbitals for Ozone
Molecular Orbitals for Ozone Purpose: In this exercise you will do semi-empirical molecular orbital calculations on ozone with the goal of understanding the molecular orbital print out provided by Spartan
To learn how to use molecular modeling software, a commonly used tool in the chemical and pharmaceutical industry.
NAME: Lab Day/Time: Molecular Modeling BV 1/2009 Purpose The purposes of this experiment are: To learn how to use molecular modeling software, a commonly used tool in the chemical and pharmaceutical industry.
Tutorial I: IQ MOL and Basic DFT and MP2 Calculations 1 / 30
Tutorial I: IQ MOL and Basic DFT and MP2 Calculations Q-Chem User Workshop, Denver March 21, 2015 1 / 30 2 / 30 Introduction to IQMOL DFT and MP2 Calculations 3 / 30 IQMOL and Q-CHEM IQMOL is an open-source
Assignment 1: Molecular Mechanics (PART 1 25 points)
Chemistry 380.37 Fall 2015 Dr. Jean M. Standard August 19, 2015 Assignment 1: Molecular Mechanics (PART 1 25 points) In this assignment, you will perform some molecular mechanics calculations using the
BOND LENGTH WITH HYPERCHEM LITE
BOND LENGTH WITH HYPERCHEM LITE LAB MOD2.COMP From Gannon University SIM INTRODUCTION The electron cloud surrounding the nucleus of the atom determines the size of the atom. Since this distance is somewhat
S N 2 reaction. Br- + ClCH 3 BrCH 3 + Cl-
FY1006 Innføring i kvantefysikk og TFY4215 Kjemisk fysikk og kvantemekanikk Spring 2012 Chemical Physics Exercise 2 To be delivered by Friday 27.04.12 S N 2 reaction. Introduction Many chemical reactions
Computational Chemistry Lab Module: Conformational Analysis of Alkanes
Introduction Computational Chemistry Lab Module: Conformational Analysis of Alkanes In this experiment, we will use CAChe software package to model the conformations of butane, 2-methylbutane, and substituted
Calculating NMR Chemical Shifts for beta-ionone O
Calculating NMR Chemical Shifts for beta-ionone O Molecular orbital calculations can be used to get good estimates for chemical shifts. In this exercise we will calculate the chemical shifts for beta-ionone.
The Hückel Approximation
The ückel Approximation 1 In this exercise you will use a program called ückel to look at the π molecular orbitals in conjugated molecules. The program calculates the energies and shapes of π (pi) molecular
Introduc)on to IQmol: Part I.!!! Shirin Faraji, Ilya Kaliman, and Anna Krylov
Introduc)on to IQmol: Part I!!! Shirin Faraji, Ilya Kaliman, and Anna Krylov! 1 Resources! Written by Dr. Andrew Gilbert Keep yourself up to date with IQmol website: http://iqmol.org! IQmol Youtube channel:
IFM Chemistry Computational Chemistry 2010, 7.5 hp LAB2. Computer laboratory exercise 1 (LAB2): Quantum chemical calculations
Computer laboratory exercise 1 (LAB2): Quantum chemical calculations Introduction: The objective of the second computer laboratory exercise is to get acquainted with a program for performing quantum chemical
Modeling the UV-Vis Absorption of a Series of Dyes CH342L: Spectroscopy February 15, 2016
Modeling the UV-Vis Absorption of a Series of Dyes CH342L: Spectroscopy February 15, 2016 We ll correlate the absorbance maximum of a series of dyes with structural changes between them 1. Chemicals absorb
Calculating Bond Enthalpies of the Hydrides
Proposed Exercise for the General Chemistry Section of the Teaching with Cache Workbook: Calculating Bond Enthalpies of the Hydrides Contributed by James Foresman, Rachel Fogle, and Jeremy Beck, York College
Computational Chemistry Using the University of Alaska WebMO Site
2/7/2017 1 Computational Chemistry Using the University of Alaska WebMO Site John Keller Department of Chemistry & Biochemistry University of Alaska Fairbanks Intro and operation of WebMO and MOPAC Basic
1s atomic orbital 2s atomic orbital 2s atomic orbital (with node) 2px orbital 2py orbital 2pz orbital
Atomic Orbitals 1s atomic orbital 2s atomic orbital 2s atomic orbital (with node) 2px orbital 2py orbital 2pz orbital Valence Bond Theory and ybridized Atomic Orbitals Bonding in 2 1s 1s Atomic Orbital
Getting Started with Spartan 3rd Edition
Getting Started with Spartan 3rd Edition WAVEFUNCTION Wavefunction, Inc. 18401 Von Karman Avenue, Suite 370 Irvine, CA 92612 U.S.A. www.wavefun.com Wavefunction, Inc., Japan Branch Office Level 14 ibiya
Chem 1 Kinetics. Objectives. Concepts
Chem 1 Kinetics Objectives 1. Learn some basic ideas in chemical kinetics. 2. Understand how the computer visualizations can be used to benefit the learning process. 3. Understand how the computer models
ICM-Chemist-Pro How-To Guide. Version 3.6-1h Last Updated 12/29/2009
ICM-Chemist-Pro How-To Guide Version 3.6-1h Last Updated 12/29/2009 ICM-Chemist-Pro ICM 3D LIGAND EDITOR: SETUP 1. Read in a ligand molecule or PDB file. How to setup the ligand in the ICM 3D Ligand Editor.
Teaching with SCIGRESS
Teaching with SCIGRESS Exercises on Molecular Modeling in Chemistry Crispin Wong and James Currie, eds. Pacific University Teaching with SCIGRES Molecular Modeling in Chemistry Crispin Wong and James Currie
Space Objects. Section. When you finish this section, you should understand the following:
GOLDMC02_132283433X 8/24/06 2:21 PM Page 97 Section 2 Space Objects When you finish this section, you should understand the following: How to create a 2D Space Object and label it with a Space Tag. How
3. An Introduction to Molecular Mechanics
3. An Introduction to Molecular Mechanics Introduction When you use Chem3D to draw molecules, the program assigns bond lengths and bond angles based on experimental data. The program does not contain real
BUILDING BASICS WITH HYPERCHEM LITE
BUILDING BASICS WITH HYPERCHEM LITE LAB MOD1.COMP From Gannon University SIM INTRODUCTION A chemical bond is a link between atoms resulting from the mutual attraction of their nuclei for electrons. There
Application Note. U. Heat of Formation of Ethyl Alcohol and Dimethyl Ether. Introduction
Application Note U. Introduction The molecular builder (Molecular Builder) is part of the MEDEA standard suite of building tools. This tutorial provides an overview of the Molecular Builder s basic functionality.
John Keller Department of Chemistry & Biochemistry University of Alaska Fairbanks
10/15/2016 1 WebMO & Gaussian John Keller Department of Chemistry & Biochemistry University of Alaska Fairbanks Corrections and updates 9-5-2017 SCHEDULE 9-10 Intro and basic operation of WebMO and MOPAC
POC via CHEMnetBASE for Identifying Unknowns
Table of Contents A red arrow is used to identify where buttons and functions are located in CHEMnetBASE. Figure Description Page Entering the Properties of Organic Compounds (POC) Database 1 CHEMnetBASE
Expt MM 1. MOLECULAR MODELING AND PREDICTIONS OF EQUILIBRIUM CONSTANT FOR MENTHONE (trans) AND ISOMENTHONE (cis) ISOMERS (MM)
Expt MM 1 MOLECULAR MODELING AND PREDICTIONS OF EQUILIBRIUM CONSTANT FOR MENTHONE (trans) AND ISOMENTHONE (cis) ISOMERS (MM) Important Modification Note the software in use may be changed in 2008 to Scigress.
Chemistry 112 Laboratory Experiment 5: Visualizing Molecular Orbitals: A MacSpartan Pro Experience (This experiment will be conducted in OR341)
Chemistry 112 Laboratory Experiment 5: Visualizing Molecular Orbitals: A MacSpartan Pro Experience (This experiment will be conducted in OR341) Introduction In class we have discussed Lewis structures,
3. An Introduction to Molecular Mechanics
3. An Introduction to Molecular Mechanics Introduction When you use Chem3D to draw molecules, the program assigns bond lengths and bond angles based on experimental data. The program does not contain real
To visualize the three-dimensional structures of some common molecules. To obtain bond angle, bond length, and hybridization data for molecules.
Molecular Geometry PURPOSE A B C To explore some simple molecular structures. To explore the relationship between bond order and bond length. To explore resonance structures. GOALS To compare Lewis structures
Experiment: Oscillations of a Mass on a Spring
Physics NYC F17 Objective: Theory: Experiment: Oscillations of a Mass on a Spring A: to verify Hooke s law for a spring and measure its elasticity constant. B: to check the relationship between the period
Dock Ligands from a 2D Molecule Sketch
Dock Ligands from a 2D Molecule Sketch March 31, 2016 Sample to Insight CLC bio, a QIAGEN Company Silkeborgvej 2 Prismet 8000 Aarhus C Denmark Telephone: +45 70 22 32 44 www.clcbio.com support-clcbio@qiagen.com
Endothermic and Exothermic Reactions
Endothermic and Exothermic Reactions Experiment 1 Many chemical reactions give off energy. Chemical reactions that release energy are called exothermic reactions. Some chemical reactions absorb energy
MO Energies and Reaction Rates Chemistry 200 Fall 2004 Assignment #10 Due: November 5, 2004, high noon
M Energies and Reaction Rates hemistry 200 all 2004 Assignment #10 Due: November 5, 2004, high noon Go through each of the problems below, and then present the answers using Microsoft Word. If structures
Hybridization of Atomic Orbitals. (Chapter 1 in the Klein text)
Hybridization of Atomic Orbitals (Chapter 1 in the Klein text) Basic Ideas The atomic structures, from the Periodic Table, of atoms such as C, N, and O do not adequately explain how these atoms use orbitals
1. Double-click the ArcMap icon on your computer s desktop. 2. When the ArcMap start-up dialog box appears, click An existing map and click OK.
Module 2, Lesson 1 The earth moves In this activity, you will observe worldwide patterns of seismic activity (earthquakes) and volcanic activity (volcanoes). You will analyze the relationships of those
In order to save time, the following data files have already been preloaded to the computer (most likely under c:\odmc2012\data\)
ODMC2012 QGIS Ex1 Schools and Public Transport In this exercise, users will learn how to a) map the location of secondary schools in and around the Southampton area; b) overlay the school location map
UNIT TWO BOOKLET 1. Molecular Orbitals and Hybridisation
DUNCANRIG SECONDARY ADVANCED HIGHER CHEMISTRY UNIT TWO BOOKLET 1 Molecular Orbitals and Hybridisation In the inorganic unit we learned about atomic orbitals and how they could be used to write the electron
OCEAN/ESS 410 Lab 4. Earthquake location
Lab 4. Earthquake location To complete this exercise you will need to (a) Complete the table on page 2. (b) Identify phases on the seismograms on pages 3-6 as requested on page 11. (c) Locate the earthquake
SeeSAR 7.1 Beginners Guide. June 2017
SeeSAR 7.1 Beginners Guide June 2017 Part 1: Basics 1 Type a pdb code and press return or Load your own protein or already existing project, or Just load molecules To begin, let s type 2zff and download
Stoichiometric Reactor Simulation Robert P. Hesketh and Concetta LaMarca Chemical Engineering, Rowan University (Revised 4/8/09)
Stoichiometric Reactor Simulation Robert P. Hesketh and Concetta LaMarca Chemical Engineering, Rowan University (Revised 4/8/09) In this session you will learn how to create a stoichiometric reactor model
Winmostar tutorial Gromacs Interfacial Tension V X-Ability Co., Ltd. 2018/01/15
Winmostar tutorial Gromacs Interfacial Tension V8.007 X-Ability Co., Ltd. question@winmostar.com Summary In this tutorial, we will calculate density distribution and interfacial tension between liquid-liquid
ICM-Chemist How-To Guide. Version 3.6-1g Last Updated 12/01/2009
ICM-Chemist How-To Guide Version 3.6-1g Last Updated 12/01/2009 ICM-Chemist HOW TO IMPORT, SKETCH AND EDIT CHEMICALS How to access the ICM Molecular Editor. 1. Click here 2. Start sketching How to sketch
Please read and sign the Honor Code statement below:
CHEM 3311 Exam #1 Name Dr. Minger June 7, 2010 Please read and sign the Honor Code statement below: I pledge that on my honor, as a University of Colorado at Boulder student, I have neither given nor received
Computational Study of Chemical Kinetics (GIDES)
Computational Study of Chemical Kinetics (GIDES) Software Introduction Berkeley Madonna (http://www.berkeleymadonna.com) is a dynamic modeling program in which relational diagrams are created using a graphical
After obtaining access to the Jmol program you should see an image on your computer screen that looks similar to the following figure. Figure 1.
A C T I V I T I E S Molecular Modeling Introduction to Molecular Modeling In the following laboratory activities you will examine three-dimensional models of molecules using the computer-based molecular
Winmostar tutorial LAMMPS Melting point V X-Ability Co,. Ltd. 2017/8/17
Winmostar tutorial LAMMPS Melting point V7.025 X-Ability Co,. Ltd. question@winmostar.com Contents Configure I. Build solid phase II. Equilibration of solid phase III. Equilibration of liquid phase IV.
LAB 2 - ONE DIMENSIONAL MOTION
Name Date Partners L02-1 LAB 2 - ONE DIMENSIONAL MOTION OBJECTIVES Slow and steady wins the race. Aesop s fable: The Hare and the Tortoise To learn how to use a motion detector and gain more familiarity
SkyGlobe Planetarium
SkyGlobe Planetarium Introduction: This exercise will simulate the night sky and demonstrate a number of principles of the celestial sphere and the motions of the Earth and planets. Getting Started: 1.
Contents. 13. Graphs of Trigonometric Functions 2 Example Example
Contents 13. Graphs of Trigonometric Functions 2 Example 13.19............................... 2 Example 13.22............................... 5 1 Peterson, Technical Mathematics, 3rd edition 2 Example 13.19
ISIS/Draw "Quick Start"
ISIS/Draw "Quick Start" Click to print, or click Drawing Molecules * Basic Strategy 5.1 * Drawing Structures with Template tools and template pages 5.2 * Drawing bonds and chains 5.3 * Drawing atoms 5.4
Chapter 2: Alkanes MULTIPLE CHOICE
Chapter 2: Alkanes MULTIPLE CHOICE 1. Which of the following orbitals is properly described as an antibonding orbital? a. sp + 1s d. sp 2 1s b. sp 2 + 1s e. sp 2 + sp 2 sp 3 + 1s D DIF: Easy REF: 2.2 2.
Lecture 16 C1403 October 31, Molecular orbital theory: molecular orbitals and diatomic molecules
Lecture 16 C1403 October 31, 2005 18.1 Molecular orbital theory: molecular orbitals and diatomic molecules 18.2 Valence bond theory: hybridized orbitals and polyatomic molecules Bond order, bond lengths,
Free Energy Change and Activation Barrier for a Menshutkin Reaction Including Effects of the Solvent
Proposed Exercise for the Physical Chemistry Section of the Teaching with Cache Workbook: Free Energy Change and Activation Barrier for a Menshutkin Reaction Including Effects of the Solvent Contributed
1. Problem 3-5 Use ChemDraw to generate the nine isomers of C 7 H 16.
Copyright 2002 Prentice-Hall, Inc. All rights reserved. Chapter 3 - Structure and Stereochemistry of Alkanes 1. Problem 3-5 Use ChemDraw to generate the nine isomers of C 7 H 16. Hint: Begin with a chain
through any three given points if and only if these points are not collinear.
Discover Parabola Time required 45 minutes Teaching Goals: 1. Students verify that a unique parabola with the equation y = ax + bx+ c, a 0, exists through any three given points if and only if these points
Covalent Bonding. Click a hyperlink or folder tab to view the corresponding slides. Exit
Covalent Bonding Section 8.1 The Covalent Bond Section 8.2 Naming Molecules Section 8.3 Molecular Structures Section 8.4 Molecular Shapes Section 8.5 Electronegativity and Polarity Click a hyperlink or
Chemistry 344 Molecular Modeling Spring 2006
1 Chemistry 344 Molecular Modeling Spring 2006 1.1 Introduction to Molecular Modeling 1.2 Problem Set A: Using Molecular Mechanics Calculations to Analyze Conformations of Hydrocarbons. 1.2.1. Butane 1.2.2.
Lab 1 Uniform Motion - Graphing and Analyzing Motion
Lab 1 Uniform Motion - Graphing and Analyzing Motion Objectives: < To observe the distance-time relation for motion at constant velocity. < To make a straight line fit to the distance-time data. < To interpret
3D - Structure Graphics Capabilities with PDF-4 Database Products
3D - Structure Graphics Capabilities with PDF-4 Database Products Atomic Structure Information in the PDF-4 Databases ICDD s PDF-4 databases contain atomic structure information for a significant number
Experiment 15: Atomic Orbitals, Bond Length, and Molecular Orbitals
Experiment 15: Atomic Orbitals, Bond Length, and Molecular Orbitals Introduction Molecular orbitals result from the mixing of atomic orbitals that overlap during the bonding process allowing the delocalization
(THIS IS AN OPTIONAL BUT WORTHWHILE EXERCISE)
PART 2: Analysis in ArcGIS (THIS IS AN OPTIONAL BUT WORTHWHILE EXERCISE) Step 1: Start ArcCatalog and open a geodatabase If you have a shortcut icon for ArcCatalog on your desktop, double-click it to start
How many states. Record high temperature
Record high temperature How many states Class Midpoint Label 94.5 99.5 94.5-99.5 0 97 99.5 104.5 99.5-104.5 2 102 102 104.5 109.5 104.5-109.5 8 107 107 109.5 114.5 109.5-114.5 18 112 112 114.5 119.5 114.5-119.5
Jaguar DFT Optimizations and Transition State Searches
Jaguar DFT Optimizations and Transition State Searches Density Functional Theory (DFT) is a quantum mechanical (QM) method that gives results superior to Hartree Fock (HF) in less computational time. A
Computer simulation of radioactive decay
Computer simulation of radioactive decay y now you should have worked your way through the introduction to Maple, as well as the introduction to data analysis using Excel Now we will explore radioactive
Covalent Bonding. Click a hyperlink or folder tab to view the corresponding slides. Exit
Covalent Bonding Section 8.1 The Covalent Bond Section 8.2 Naming Molecules Section 8.3 Molecular Structures Section 8.4 Molecular Shapes Section 8.5 Electronegativity and Polarity Click a hyperlink or
EXAMINATION 1 Chemistry 3A
1 EXAMINATION 1 Chemistry 3A Name: Key Print first name before second! Use capital letters! SID #: Peter Vollhardt February 18, 2016 GSI (if you are taking Chem 3AL): Please provide the following information
Introduction to Astronomy Laboratory Exercise #1. Intro to the Sky
Introduction to Astronomy Laboratory Exercise #1 Partners Intro to the Sky Date Section Purpose: To develop familiarity with the daytime and nighttime sky through the use of Stellarium. Equipment: Computer
Lecture 1. Conformational Analysis in Acyclic Systems
Lecture 1 Conformational Analysis in Acyclic Systems Learning Outcomes: by the end of this lecture and after answering the associated problems, you will be able to: 1. use Newman and saw-horse projections
Semi-Empirical MO Methods
Semi-Empirical MO Methods the high cost of ab initio MO calculations is largely due to the many integrals that need to be calculated (esp. two electron integrals) semi-empirical MO methods start with the
1. It can help us decide which of several Lewis dot structures is closest to representing the properties of the real compound.
Molecular Structure Properties The electron was discovered in the year of 1900, and it took about twenty years for the electronic nature of the chemical bond to come into wide acceptance. Particle-based
iworx Sample Lab Experiment GB-2: Membrane Permeability
Experiment GB-2: Membrane Permeability Exercise 1: Movement of Small Positive Ions Across a Membrane Aim: To determine if small, positively charged, hydrogen ions can move across a membrane from a region
CHEMDRAW ULTRA ITEC107 - Introduction to Computing for Pharmacy. ITEC107 - Introduction to Computing for Pharmacy 1
CHEMDRAW ULTRA 12.0 ITEC107 - Introduction to Computing for Pharmacy 1 Objectives Basic drawing skills with ChemDraw Bonds, captions, hotkeys, chains, arrows Checking and cleaning up structures Chemical
experiment11 Molecular Structures
59 experiment11 OBJECTIVES To determine the number of valence electrons in molecules. To determine the Lewis structure of molecules. To determine the electron pair geometry and geometry (shape) of molecules.
Tutorial. Getting started. Sample to Insight. March 31, 2016
Getting started March 31, 2016 Sample to Insight CLC bio, a QIAGEN Company Silkeborgvej 2 Prismet 8000 Aarhus C Denmark Telephone: +45 70 22 32 44 www.clcbio.com support-clcbio@qiagen.com Getting started
PQSMol. User s Manual
PQSMol User s Manual c Parallel Quantum Solutions, 2006 www.pqs-chem.com Conventions used in this manual Filenames, commands typed in at the command prompt are written in typewriter font: pqsview aspirin.out
Covalent Bonding. Click a hyperlink or folder tab to view the corresponding slides. Exit
Covalent Bonding Section 8.1 The Covalent Bond Section 8.2 Naming Molecules Section 8.3 Molecular Structures Section 8.4 Molecular Shapes Section 8.5 Electronegativity and Polarity Click a hyperlink or
Viewing and Analyzing Proteins, Ligands and their Complexes 2
2 Viewing and Analyzing Proteins, Ligands and their Complexes 2 Overview Viewing the accessible surface Analyzing the properties of proteins containing thousands of atoms is best accomplished by representing
ADF-GUI Tutorial. ADF Program System Release
ADF-GUI Tutorial ADF Program System Release 2009.01 Scientific Computing & Modelling NV Vrije Universiteit, Theoretical Chemistry De Boelelaan 1083; 1081 HV Amsterdam; The Netherlands E-mail: support@scm.com
MOHID Land Basics Walkthrough Walkthrough for MOHID Land Basic Samples using MOHID Studio
ACTION MODULERS MOHID Land Basics Walkthrough Walkthrough for MOHID Land Basic Samples using MOHID Studio Frank Braunschweig Luis Fernandes Filipe Lourenço October 2011 This document is the MOHID Land
Class Activity 5A. Conformations of Alkanes Part A: Acyclic Compounds
Class Activity 5a Conformations of Alkanes Part A: Acyclic Compounds 1 Model 1: Isomers Class Activity 5A Conformations of Alkanes Part A: Acyclic Compounds C C O C C C C C C C O O A B C wedge, bond coming