Jack Smith. Center for Environmental, Geotechnical and Applied Science. Marshall University
|
|
|
- Tracey Thompson
- 5 years ago
- Views:
Transcription
1 Jack Smith Center for Environmental, Geotechnical and Applied Science Marshall University -- Division of Science and Research WV Higher Education Policy Commission WVU HPC Summer Institute June 20, 2014
2 Outline Accessing WebMO on Marshall s HPC cluster Overview of WebMO capabilities Building molecules Submitting jobs Optimizing a geometry Electronic properties Visualizing orbitals, densities, and electrostatic potential IR spectrum and animating the vibrational modes UV-Vis spectrum Geometry scan, transition state, and reaction pathway Future topics Exercises
3 Accessing WebMO Non-Marshall people will first need to apply for MU ID Contact Ed Aractingi at for form Apply for account on HPC cluster Use form at: Select Jack Smith as sponsor Check yes for access to WebMO on form Already have an HPC cluster account, but no WebMO access? Contact Jack Smith at for WebMO access Log in to WebMO with web browser Use your regular MU login credentials Browser needs recent Java plug-in for 3D editor WebMO now available as an app for ipad ($4.99) Still needs access to WebMO account on cluster
4 Accessing WebMO * as workshop student only * Log in to WebMO with web browser Use username provided by instructor (e.g., student01) Password will also be provided by instructor Accounts will expire at the end of the HPC Summer Institute Browser needs recent Java plug-in for 3D editor
5 Accessing WebMO Login
6 Accessing WebMO Job Manager
7 WebMO Capabilities Supports many computational engines GAUSSIAN, GAMESS, MOPAC, Tinker, NWChem, Quantum Espresso, VASP, MolPro, PQS, PSI, QChem GUI is completely browser-based (+Java 3D) Built-in 3D molecular editor Batch (PBS, SGE, built-in) job submission and management Visualization of results Tabulation of results Upload/download files from/to desktop See WebMO website for more info:
8 WebMO Capabilities Calculation Types Single-point energy calculation Geometry optimization Electronic properties Molecular orbitals, partial charges, dipole moment Geometry scan Conformational analysis, reaction coordinates IR spectrum (vibrational analysis) UV-Vis spectrum (excitations) NMR spectrum (chemical shifts, shielding) Thermochemistry and model chemistries
9 WebMO Capabilities Levels of Theory Molecular Mechanics No electrons! No breaking or forming bonds! Forcefields: MM3, Semi-empirical (Quantum Mechanical) HF with parameterized integrals Fit to Heats of Formation Density Functional Theory No wavefunction! Approximate exchange-correlation: B3LYP, Ab initio (Wave Function) HF no electron correlation! Correlation: CI, MP, MBPT, CC, Tinker MOPAC GAMESS NWChem GAUSSIAN :
10 Building Molecules Use build tool to click and drag atoms and bonds Use build menu (or periodic table) to change element or add a pre-defined fragment Use right-click context menu to change element hybridization/charge or bond order Use cleanup tool/menu to add Hydrogens, assign hybridizations, and clean up geometry Use rotate, translation and zoom tools to manipulate view Use adjust tool and shift-click to select atoms, bonds, angles or dihedrals and modify their values Check status line for current tool/view mode and available mouse/keyboard options
11 Building Molecules
12 Building Molecules
13 Submitting Jobs Choose Computational Engine GAMESS, Gaussian, NWChem, MOPAC, Tinker Configure Job Options Name Calculation Type Level of Theory DFT Functional (for DFT) Basis Set Charge Spin Multiplicity Submit to queue Monitor in Job Manager
14 Submitting Jobs Choose Computational Engine
15 Submitting Jobs Configure Job Options
16 Submitting Jobs Monitor Status
17 Viewing Results Molecular Viewer Final structure View properties Partial charges, dipole moment Animation Geometry optimization, vibrational modes Input for next job Data Viewer Linear plots Spectra (IR, UV-Vis, NMR) 2D maps MO Viewer (tabbed) Isosurfaces of MO s and density Texturing with other properties Electrostatic potential Frontier density (electrophilic, nucleophilic and radical susceptabilities)
18 Viewing Results Molecular Viewer
19 Viewing Results Calculated Quantities
20 Viewing Results Partial Charges
21 Viewing Results Geometry Optimization
22 Viewing Results Data Viewer
23 Viewing Results Molecular Orbitals HOMO LUMO
24 Viewing Results MO Viewer
25 Viewing Results Display Options
26 Viewing Results Vibrational Modes
27 Viewing Results Animation of Vibrational Mode
28 Viewing Results IR Spectrum
29 Viewing Results Single (UV-Vis) Excitations
30 Viewing Results UV-Vis Spectrum
31 Potential Energy Surface Geometry scans (PES) 1 or 2 internal coordinates (distance, angle, dihedral) Transition state optimization Saddle point Gradient minimization Confirm one imaginary frequency Reaction Coordinate (path) IRC: Intrinsic, kinetic energy dissipated DRC: Dynamic, T+V conserved not in WebMO!
32 Viewing Results Transition State
33 Viewing Results 2-D Geometry Scan
34 Viewing Results 2-D Geometry Scan
35 Potential Future Topics Periodic Systems and Materials Modeling Quantum ESPRESSO, VASP Reactivity, QSAR/QSPR Spectroscopy and Excited States Thermochemistry and Model Chemistries Solvation Kinetics Computational Chemistry Theory & Practice Beyond WebMO Molecular Dynamics Biomolecules (proteins, nucleic acids) Hybrid QM/MM Techniques
36 Exercise #1 Triflouroacetic acid (TFA): CF 3 COOH Build molecule in 3D editor Optimize geometry at different levels of theory MM3 (Tinker), PM3 (MOPAC), RHF/3-21G, DFT/B3LYP/6-31G(d) (GAMESS) Visualize optimization Visualize partial charges (especially acidic H), dipole moment Visualize orbitals, total and frontier densities, electrostatic potential Browse output files Perform geometry scan of C-C-O-H dihedral Visualize scan and confirm low-energy conformation Compute and visualize IR spectrum Animate vibrational nodes Compute deprotonation energy CF 3 COOH [+ H 2 O] CF 3 COO - [+ H 3 O + ] Repeat with solvent (H 2 O) Bonus: Compare acidities of CF n H 3-n COOH (n=0,3) Use MOPAC (PM3)
37 Exercise #2 Conjugated aldehyde (enal): H 2 C(=CH-CH) n =O For n = 1 (acrolein) Build and optimize structure Use MOPAC (PM3) Compute and visualize HOMO and LUMO orbitals (and those nearby) Use GAMESS: Molecular Orbitals, DFT/B3LYP/6-31G(d) Calculate HOMO-LUMO gap (1 hartree = ev) and save Compute and visualize UV-Vis (excitation) spectrum Use GAMESS: UV-Vis Spectrum, 6-31G(d) -- ignores level of theory Look at raw output for excitation details (e.g., HOMO LUMO) Compare excitation energies with HOMO-LUMO gap 1240/λ(nm) = 1 ev Repeat above for n = 2, 3 Save results in a spreadsheet and plot HOMO-LUMO gap vs excitation energies Save results as HTML (web pages) and view in browser Compare with experiment: 209, 221, 251 (nm) Bonus: Predict and test results for n > 3
38 Exercise #3 Keto-enol tautomerization (proton migration) H 3 C-C=O (acetaldehyde) H 2 C=C-OH (vinyl alcohol) Build and optimize acetaldehyde structure Convert acetaldehyde to vinyl alcohol Adding, deleting, and changing bonds only no adding/deleting atoms Clean hybridization and geometry only do not add Hydrogens Optimize vinyl alcohol structure Remember job# Return to acetaldehyde structure and compute the Saddle Point Use job# of vinyl alcohol results as second geometry Edit such that H-O-C-C forms a 4-membered ring of single bonds Optimize as a Transition State (TS) Compute vibrational frequencies Look for one negative (imaginary) frequency and animate it All at the MOPAC (PM3) Level Compute IRCs from the TS to both acetaldehyde and vinyl alcohol
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.
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
CHEM 344 Molecular Modeling
CHEM 344 Molecular Modeling The Use of Computational Chemistry to Support Experimental Organic Chemistry Part 1: Molecular Orbital Theory, Hybridization, & Formal Charge * all calculation data obtained
Using Web-Based Computations in Organic Chemistry
10/30/2017 1 Using Web-Based Computations in Organic Chemistry John Keller UAF Department of Chemistry & Biochemistry The UAF WebMO site Practical aspects of computational chemistry theory and nomenclature
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
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
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
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
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.
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
NH 3 inversion: Potential energy surfaces and transition states CH342L March 28, 2016
N 3 inversion: Potential energy surfaces and transition states C342L March 28, 2016 Last week, we used the IR spectrum of ammonia to determine the splitting of energy levels due to inversion of the umbrella
NMR and IR spectra & vibrational analysis
Lab 5: NMR and IR spectra & vibrational analysis A brief theoretical background 1 Some of the available chemical quantum methods for calculating NMR chemical shifts are based on the Hartree-Fock self-consistent
Session 1. Introduction to Computational Chemistry. Computational (chemistry education) and/or (Computational chemistry) education
Session 1 Introduction to Computational Chemistry 1 Introduction to Computational Chemistry Computational (chemistry education) and/or (Computational chemistry) education First one: Use computational tools
Q-Chem Workshop. Doubletree Hotel 2085 S. Harbor Boulevard Anaheim, CA March 26, Schedule
Q-Chem Workshop Doubletree Hotel 2085 S. Harbor Boulevard Anaheim, CA 92802 March 26, 2011 1 8:30 Schedule Welcome remarks, Prof. Peter Gill, Australian National Univ and President of Q-Chem 8:45-9:15
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
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
Patrick Lestrange and James B. Foresman, York College of PA C 9 C 10 C 11 C 12 O 13 H 14
Physical Chemistry I Laboratory: Conformational Analysis of N-Boc-3-pyrrolidinol Patrick Lestrange and James B. Foresman, York College of PA C 2 C 10 C 9 O 5 C 1 C 4 C 11 C 12 N 8 C 6 C 3 O 13 O 7 H 14
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
Computational Chemistry Problem Set 3 Due Monday, February 16, 2009 (at the start of class) Total Possible Points = 69
Computational Chemistry Problem Set 3 Due Monday, ebruary 16, 2009 (at the start of class) Total Possible Points = 69 Basic Technical Notes: (1) or security reasons, you are allowed to log into the ope
Figure 1: Transition State, Saddle Point, Reaction Pathway
Computational Chemistry Workshops West Ridge Research Building-UAF Campus 9:00am-4:00pm, Room 009 Electronic Structure - July 19-21, 2016 Molecular Dynamics - July 26-28, 2016 Potential Energy Surfaces
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
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:
Computational Chemistry Problem Set 3 Due Tuesday, February 15, 2011 (at the start of class) Total Possible Points = 69
Computational Chemistry Problem Set 3 Due Tuesday, ebruary 15, 2011 (at the start of class) Total Possible Points = 69 Basic Technical Notes: (1) or security reasons, you are allowed to log into the ope
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
Lab #5: Electron Densities, Electrostatic Potentials, and Reactivity Indices
Lab #5: Electron Densities, Electrostatic Potentials, and Reactivity Indices Exercise 1 - Visualizing Different Bond Types Build H 2 and perform a geometry optimization (Mopac) using the choices shown
Practical 1: Structure and electronic properties of organic molecules. B/ Structure, electronic and vibrational properties of the water molecule
D1CH9116 - MMCO Molecular Modelling applied to organic chemistry Practical 1: tructure and electronic properties of organic molecules B/ tructure, electronic and vibrational properties of the water molecule
Computational Chemistry Problem Set 4 Due Monday, February 22, 2011 (at the start of class) Total Number of Points = 85
Computational Chemistry Problem Set 4 Due Monday, February 22, 2011 (at the start of class) Total Number of Points = 85 Basic Technical Notes: (1) For security reasons, you are allowed to log into the
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
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
Transition states and reaction paths
Transition states and reaction paths Lab 4 Theoretical background Transition state A transition structure is the molecular configuration that separates reactants and products. In a system with a single
1 Introduction to Computational Chemistry (Spartan)
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
Lab #3: Choice of Theoretical Method
Lab #3: Choice of Theoretical Method These directions assume the user is familiar with the WebMO interface and can build molecules, set up calculations, etc. Exercise 1 - Determine the Proton Affinity
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
QUANTUM CHEMISTRY WITH GAUSSIAN : A VERY BRIEF INTRODUCTION (PART 2)
QUANTUM CHEMISTRY WITH GAUSSIAN : A VERY BRIEF INTRODUCTION (PART 2) TARAS V. POGORELOV AND MIKE HALLOCK SCHOOL OF CHEMICAL SCIENCES, UIUC This tutorial continues introduction to Gaussian [2]. Here we
Project 2. Chemistry of Transient Species in Planetary Atmospheres: Exploring the Potential Energy Surfaces of CH 2 S
Chemistry 362 Spring 2018 Dr. Jean M. Standard March 21, 2018 Project 2. Chemistry of Transient Species in Planetary Atmospheres: Exploring the Potential Energy Surfaces of CH 2 S In this project, you
Advanced Electronic Structure Theory Density functional theory. Dr Fred Manby
Advanced Electronic Structure Theory Density functional theory Dr Fred Manby fred.manby@bris.ac.uk http://www.chm.bris.ac.uk/pt/manby/ 6 Strengths of DFT DFT is one of many theories used by (computational)
CHEM 344 Molecular Modeling
CHEM 344 Molecular Modeling The Use of Computational Chemistry to Support Experimental Organic Chemistry Day 1 all calculation data obtained from Gaussian09 using B3LYP/6-31G(d) unless otherwise noted.
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
计算物理作业二. Excercise 1: Illustration of the convergence of the dissociation energy for H 2 toward HF limit.
计算物理作业二 Excercise 1: Illustration of the convergence of the dissociation energy for H 2 toward HF limit. In this exercise, basis indicates one of the following basis sets: STO-3G, cc-pvdz, cc-pvtz, cc-pvqz
Appendix D Simulating Spectroscopic Bands Using Gaussian and PGopher
429 Appendix D Simulating Spectroscopic Bands Using Gaussian and PGopher This appendix contains methods for using Gaussian 09 121 and PGopher 120 to simulate vibrational and electronic bands of molecules.
Chemistry 4560/5560 Molecular Modeling Fall 2014
Final Exam Name:. User s guide: 1. Read questions carefully and make sure you understand them before answering (if not, ask). 2. Answer only the question that is asked, not a different question. 3. Unless
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,
Chemistry 5021/8021 Computational Chemistry 3/4 Credits Spring Semester 2000 ( Due 4 / 3 / 00 )
Chemistry 5021/8021 Computational Chemistry 3/4 Credits Spring Semester 2000 ( Due 4 / 3 / 00 ) This problem set will take longer than the last one in the sense that you may need to submit some jobs, leave,
SCIGRESS Release Notes
SCIGRESS Release Notes SCIGRESS 2.9 (3.4) General-purpose quantum-chemical package niedoida available on Windows, Linux and MacOS. New methods implemented: o Ab initio: HF, MP2. o DFT: SVWN, BLYP, B3LYP,
CHAPTER 9 THEORY OF RESONANCE BY, G.DEEPA
CHAPTER 9 THEORY OF RESONANCE BY, G.DEEPA Conjugation in Alkadienes and Allylic Systems conjugation a series of overlapping p orbitals The Allyl Group allylic position is the next to a double bond 1 allyl
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
Density Functional Theory
Chemistry 380.37 Fall 2015 Dr. Jean M. Standard October 28, 2015 Density Functional Theory What is a Functional? A functional is a general mathematical quantity that represents a rule to convert a function
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,
Assignment A02: Geometry Definition: File Formats, Redundant Coordinates, PES Scans
Assignment A02: Geometry Definition: File Formats, Redundant Coordinates, PES Scans In Assignments A00 and A01, you familiarized yourself with GaussView and G09W, you learned the basics about input (GJF)
An Introduction to Quantum Chemistry and Potential Energy Surfaces. Benjamin G. Levine
An Introduction to Quantum Chemistry and Potential Energy Surfaces Benjamin G. Levine This Week s Lecture Potential energy surfaces What are they? What are they good for? How do we use them to solve chemical
Gustavus Adolphus College. Lab #5: Computational Chemistry
CHE 372 Gustavus Adolphus College Lab #5: Computational Chemistry Introduction In this investigation we will apply the techniques of computational chemistry to several of the molecular systems that we
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.
Computational Chemistry. An Introduction to Molecular Dynamic Simulations
Computational Chemistry An Introduction to Molecular Dynamic Simulations Computational chemistry simulates chemical structures and reactions numerically, based in full or in part on the fundamental laws
Preparing a PDB File
Figure 1: Schematic view of the ligand-binding domain from the vitamin D receptor (PDB file 1IE9). The crystallographic waters are shown as small spheres and the bound ligand is shown as a CPK model. HO
Chemistry 4021/8021 Computational Chemistry 3/4 Credits Spring Semester 2007 Key PS3
Chemistry 4021/8021 Computational Chemistry 3/4 Credits Spring Semester 2007 Key PS3 1. Below are two isomeric geometries that we previously examined in Problem Sets 1 and 2 as both C 10 H 16 and Si 10
Department of Chemistry. The Intersection of Computational Chemistry and Experiment
Department of Chemistry The Intersection of Computational Chemistry and Experiment Structure, Vibrational and Electronic Spectra of Organic Molecules Angelo R. Rossi Department of Chemistry The University
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
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
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
Project 1 Report File: Chem4PB3_project_1_2017-solutions last changed: 02-Feb-2017
Project 1 Report File: Chem4PB3_project_1_2017-solutions last changed: 02-Feb-2017 1. Formaldehyde comparison of results from different methods Yellow shaded boxes are closest to experimental Method #e-
Quantum Chemistry. NC State University. Lecture 5. The electronic structure of molecules Absorption spectroscopy Fluorescence spectroscopy
Quantum Chemistry Lecture 5 The electronic structure of molecules Absorption spectroscopy Fluorescence spectroscopy NC State University 3.5 Selective absorption and emission by atmospheric gases (source:
Chem 1140; Molecular Modeling
P. Wipf 1 Chem 1140 $E = -! (q a + q b )" ab S ab + ab!k
----- Ver October 24, 2014 Bug about reading MOPAC2012 Ver.14 calculations of 1 atom and 2 atoms molecule was fixed.
***** Facio's Release History ***** ----- Ver.18.8.2 ----- October 24, 2014 Bug about reading MOPAC2012 Ver.14 calculations of 1 atom and 2 atoms molecule was fixed. ----- Ver.18.8.1 ----- August 14, 2014
Chapter: 22. Visualization: Making INPUT File and Processing of Output Results
Chapter: 22 Visualization: Making INPUT File and Processing of Output Results Keywords: visualization, input and output structure, molecular orbital, electron density. In the previous chapters, we have
MO Calculation for a Diatomic Molecule. /4 0 ) i=1 j>i (1/r ij )
MO Calculation for a Diatomic Molecule Introduction The properties of any molecular system can in principle be found by looking at the solutions to the corresponding time independent Schrodinger equation
Introduction to Hartree-Fock calculations using ORCA and Chemcraft
Introduction to Hartree-Fock calculations using ORCA and Chemcraft In this exercise, you will get to use software for carrying out calculations of wavefunctions for molecules, the ORCA program. While ORCA
Quantum Chemical Simulations and Descriptors. Dr. Antonio Chana, Dr. Mosè Casalegno
Quantum Chemical Simulations and Descriptors Dr. Antonio Chana, Dr. Mosè Casalegno Classical Mechanics: basics It models real-world objects as point particles, objects with negligible size. The motion
Example questions for Molecular modelling (Level 4) Dr. Adrian Mulholland
Example questions for Molecular modelling (Level 4) Dr. Adrian Mulholland 1) Question. Two methods which are widely used for the optimization of molecular geometies are the Steepest descents and Newton-Raphson
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
Conformational energy analysis
Lab 3 Conformational energy analysis Objective This computational project deals with molecular conformations the spatial arrangement of atoms of molecules. Conformations are determined by energy, so the
CHEM 344 Fall 2016 Spectroscopy and WebMO Exam (75 pts)
CHEM 344 Fall 2016 Spectroscopy and WebMO Exam (75 pts) Name: TA Name: Exam Length = 90 min DO NOT REMOVE ANY PAGES FROM THIS EXAM PACKET. Directions for drawing molecules, reactions, and electron-pushing
Investigation 5: Infrared Spectroscopy and Molecular Modeling
2012-13 Chemistry 120 and Chem110/IR&Modeling/Procedure 1 Investigation 5: Infrared Spectroscopy and Molecular Modeling Question: What do molecules look like and how do they move? How can we make them
Vibrations of Carbon Dioxide and Carbon Disulfide
Vibrations of Carbon Dioxide and Carbon Disulfide Purpose Vibration frequencies of CO 2 and CS 2 will be measured by Raman and Infrared spectroscopy. The spectra show effects of normal mode symmetries
Computational Methods. Chem 561
Computational Methods Chem 561 Lecture Outline 1. Ab initio methods a) HF SCF b) Post-HF methods 2. Density Functional Theory 3. Semiempirical methods 4. Molecular Mechanics Computational Chemistry " Computational
Excited States Calculations for Protonated PAHs
52 Chapter 3 Excited States Calculations for Protonated PAHs 3.1 Introduction Protonated PAHs are closed shell ions. Their electronic structure should therefore be similar to that of neutral PAHs, but
Advanced Electronic Structure Theory Density functional theory. Dr Fred Manby
Advanced Electronic Structure Theory Density functional theory Dr Fred Manby fred.manby@bris.ac.uk http://www.chm.bris.ac.uk/pt/manby/ Course overview This is a course about density functional theory (DFT)
Q-Chem Workshop Tasks
Marek Freindorf Q-Chem Workshop Tasks Washington DC August 2009 Basic Calculations Carbon Dioxide, Example 1A 1. Calculate an optimal geometry of carbon dioxide using the B3LYP/6-31+G* level of theory
Exercise 1: Structure and dipole moment of a small molecule
Introduction to computational chemistry Exercise 1: Structure and dipole moment of a small molecule Vesa Hänninen 1 Introduction In this exercise the equilibrium structure and the dipole moment of a small
Walter Kohn was awarded with the Nobel Prize in Chemistry in 1998 for his development of the density functional theory.
Walter Kohn was awarded with the Nobel Prize in Chemistry in 1998 for his development of the density functional theory. Walter Kohn receiving his Nobel Prize from His Majesty the King at the Stockholm
Bond Polarity Activity AP Chemistry 2 points Date: Hour: In this activity, you will learn about bond polarity using the online software WebMO.
Bond Polarity Activity Name: AP Chemistry 2 points Date: Hour: In this activity, you will learn about bond polarity using the online software WebMO. Background Knowledge: 1) What types of chemical bonds
Spring Term 2012 Dr. Williams (309 Zurn, ex 2386)
Chemistry 242 Organic Chemistry II Spring Term 2012 Dr. Williams (309 Zurn, ex 2386) Web Page: http://math.mercyhurst.edu/~jwilliams/ jwilliams@mercyhurst.edu (or just visit Department web site and look
Computational chemistry with GAMESS: a very brief overview with examples
Computational chemistry with GAMESS: a very brief overview with examples PHY-6120 Molecular Physics (Spring 2015), UConn Phys. Dept. Feb 17 th 2015 H = ħ2 2μ i Intro: V(R) for diatomic molecules + k Z
Last Name or Student ID
11/05/18, Chem433 Exam # 2 Last ame or Student ID 1. (2 pts) 2. (9 pts) 3. (2 pts) 4. (2 pts) 5. (2 pts) 6. (2 pts) 7. (2 pts) 8. (4 pts) 9. (14 pts) 10. (10 pts) 11. (26/31 pts) 12. (25/27 pts) Extra
Molecular Modelling for Medicinal Chemistry (F13MMM) Room A36
Molecular Modelling for Medicinal Chemistry (F13MMM) jonathan.hirst@nottingham.ac.uk Room A36 http://comp.chem.nottingham.ac.uk Assisted reading Molecular Modelling: Principles and Applications. Andrew
Computational and spectroscopic investigation of 7-azaindole: Solvation and intermolecular interactions
Computational and spectroscopic investigation of 7-azaindole: Solvation and intermolecular interactions Michael Kamrath, Krista Cruse, Nathan Erickson, Molly Beernink Abstract We report results of an experimental
Introduction to computational chemistry Exercise I: Structure and electronic energy of a small molecule. Vesa Hänninen
Introduction to computational chemistry Exercise I: Structure and electronic energy of a small molecule Vesa Hänninen 1 Introduction In this exercise the equilibrium structure and the electronic energy
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.
Organic Chemistry 112 A B C - Syllabus Addendum for Prospective Teachers
Chapter Organic Chemistry 112 A B C - Syllabus Addendum for Prospective Teachers Ch 1-Structure and bonding Ch 2-Polar covalent bonds: Acids and bases McMurry, J. (2004) Organic Chemistry 6 th Edition
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
DFT calculations of NMR indirect spin spin coupling constants
DFT calculations of NMR indirect spin spin coupling constants Dalton program system Program capabilities Density functional theory Kohn Sham theory LDA, GGA and hybrid theories Indirect NMR spin spin coupling
Calculate a rate given a species concentration change.
Kinetics Define a rate for a given process. Change in concentration of a reagent with time. A rate is always positive, and is usually referred to with only magnitude (i.e. no sign) Reaction rates can be
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.
Tuning Color Through Substitution
1 Tuning Color Through Substitution Introduction In this experiment, the effect of substituents on the absorbance spectra of molecules will be related to the structure of the molecular orbitals involved
Investigation 5: Infrared Spectroscopy and Molecular Modeling
2014 Chemistry 120 and Chem110/IR&Modeling/Procedure 1 Investigation 5: Infrared Spectroscopy and Molecular Modeling Question: What do molecules look like and how do they move? How can we make them vibrate?
Hints on Using the Orca Program
Computational Chemistry Workshops West Ridge Research Building-UAF Campus 9:00am-4:00pm, Room 009 Electronic Structure - July 19-21, 2016 Molecular Dynamics - July 26-28, 2016 Hints on Using the Orca Program
7a. Structure Elucidation: IR and 13 C-NMR Spectroscopies (text , , 12.10)
2009, Department of Chemistry, The University of Western Ontario 7a.1 7a. Structure Elucidation: IR and 13 C-NMR Spectroscopies (text 11.1 11.5, 12.1 12.5, 12.10) A. Electromagnetic Radiation Energy is
An Initio Theoretical Study for the Electronic Spectra of β-thioxoketones
American Journal of Applied Sciences 9 (1): 152-157, 2012 ISSN 1546-9239 2012 Science Publications An Initio Theoretical Study for the Electronic Spectra of β-thioxoketones 1 Rita S. Elias, 2 Bahjat A.
XYZ file format Protein Data Bank (pdb) file format Z - matrix
Chemistry block (exercise 1) In this exercise, students will be introduced how to preform simple quantum chemical calculations. Input files for Gaussian09. Output file structure. Geometry optimization,
Physical Chemistry Lab: The Hydrolysis of Aspirin. Each collaborative team determines the rate constant for the hydrolysis of aspirin.
CH 348 Physical Chemistry Spring 2009 MK Bowman Adapted from: Marrs, Peter S. J. Chem. Educ. 2004 81 870. Physical Chemistry Lab: The Hydrolysis of Aspirin Each collaborative team determines the rate constant
1.1 Is the following molecule aromatic or not aromatic? Give reasons for your answer.
Page 1 QUESTION ONE 1.1 Is the following molecule aromatic or not aromatic? Give reasons for your answer. 1.2 List four criteria which compounds must meet in order to be considered aromatic. Page 2 QUESTION