SCM: COSMO-RS GUI Tutorial

Description

COSMO-RS GUI Tutorial
ADF Program System
Release 2010
Scientific Computing & Modelling NV
Vrije Universiteit, Theoretical Chemistry
De Boelelaan 1083; 1081 HV Amsterdam; The Netherlands
E-mail: [e-mail]
Copyright © 1993-2010: SCM / Vrije Universiteit, Theoretical Chemistry, Amsterdam, The Netherlands
All rights reserved
1Table of Contents
COSMO-RS GUI Tutorial ................................................................................................................................ 1 ........................................................................................................................................... 2
Introduction..................................................................................................................................................... 3
The COSMO-RS GUI module ADFcrs .................................................................................................. 3
ADF installation ..................................................................................................................................... 3
UNIX (such as Linux) users............................................................................................................ 3
Windows users ............................................................................................................................... 4
Macintosh users ......................................................................................................... ...

Sujets

• Tutoriel
• Agent de calcul
• Éthanol
• Union nationale des associations de défense des familles et de l'individu
• Axe de polarité
• Tant pis ! Tant mieux !

Informations

• Publié par: Ummo
• Nombre de lectures: 108
• Langue: English
• Poids de l'ouvrage: 2 Mo

Extrait

COSMO-RS GUI Tutorial

ADF Program System Release 2010

Scientific Computing & Modelling NV Vrije Universiteit, Theoretical Chemistry De Boelelaan 1083; 1081 HV Amsterdam; The Netherlands E-mail:ocmcs.mro@tppsu

Copyright © 1993-2010: SCM / Vrije Universiteit, Theoretical Chemistry, Amsterdam, The Netherlands All rights reserved

1

Table of Contents

COSMO-RS GUI Tutorial ................................................................................................................................ 1 Table of Contents ........................................................................................................................................... 2 Introduction..................................................................................................................................................... 3 The COSMO-RS GUI module ADFcrs .................................................................................................. 3 ADF installation ..................................................................................................................................... 3 UNIX (such as Linux) users............................................................................................................ 3 Windows users ............................................................................................................................... 4 Macintosh users ............................................................................................................................. 4 Tutorials .......................................................................................................................................................... 5 Tutorial 1: COSMO result files.............................................................................................................. 5 Step 1: Start ADFinput ................................................................................................................... 5 Step 2: Create the molecule ........................................................................................................... 5 Step 3: Optimize the gas phase geometry ..................................................................................... 6 Step 4: Set up the COSMO parameters ......................................................................................... 8 Step 5: Perform the COSMO calculation and obtain the COSMO result file ................................ 11 Tutorial 2: COSMO-RS overview: analysis ....................................................................................... 12 Step 1: Copy COSMO result Files................................................................................................ 12 Step 2: Start ADFcrs..................................................................................................................... 12 Step 3: Add Compounds .............................................................................................................. 13 Step 4: Set pure compound parameters ...................................................................................... 15 Step 5: Set the COSMO-RS parameters ...................................................................................... 16 Step 6: Visualize the COSMO surface: ADFview ......................................................................... 17 Step 7: Analysis: The sigma profile .............................................................................................. 19 Step 8: Analysis: The sigma potential .......................................................................................... 20 Tutorial 3: COSMO-RS overview: properties .................................................................................... 23 Step 1: Start ADFcrs..................................................................................................................... 23 Step 2: Calculate a solvent vapor pressure.................................................................................. 23 Step 3: Calculate the boiling point of a solvent ............................................................................ 25 Step 4: Calculate partition coefficients (log P) .............................................................................. 27 Step 5: Calculate activity coefficients ........................................................................................... 29 Step 6: Calculate solubility ........................................................................................................... 31 Step 7: Calculate binary mixtures VLE/LLE ................................................................................. 33 Isothermal............................................................................................................................ 33 Isothermal, input pure compound vapor pressure ............................................................... 36 Isobaric ................................................................................................................................ 39 Tutorial 4: Examples using the COSMO-RS database ..................................................................... 40 4.1: How to use the COSMO-RS database .................................................................................. 40 Step 1: Add compounds ...................................................................................................... 40 Step 2: Select a compound ................................................................................................. 41 Step 3: Visualize the COSMO surface: ADFview ................................................................ 43 4.2: Octanol-Water partition coefficients (log P OW )...................................................................... 43 4.3: Henry's law constants............................................................................................................ 45 4.4: Solubility of Vanillin in organic solvents................................................................................. 50 4.5: Binary mixture of Methanol and Hexane ............................................................................... 52 4.6: Large infinite dilution activity coefficients in Water ................................................................ 54 4.7: Parametrization of ADF COSMO-RS: ΔG hydr , vapor pressures, partition coefficients.......... 57 Tutorial 5: pK a values ......................................................................................................................... 63 5.1: Empirical pK a calculation method.......................................................................................... 63 5.2: Relative pK a calculation method ........................................................................................... 66 Tutorial Videos.............................................................................................................................................. 67

2

Introduction

This document will provide a hands-on tutorial demonstrating the COSMO-RS GUI. Its purpose is to give a quick tour of the main features of the COSMO-RS GUI.

The first tutorial describes how to create COSMO result files that are needed as input for the COSMO-RS calculation. The second tutorial describes some analysis tools (sigma profile, sigma potential), and shows how to set COSMO-RS parameters. The third tutorial describes how to calculate properties, such as solvent vapor pressures, solvent boiling points, partition coefficients (log P), activity coefficients, solvation free energies, Henry's law coefficients, solubilities, vapor liquid diagrams binary mixture (VLE/LLE), and excess energies. The fourth tutorial describes how to use the COSMO-RS database ADFCRS-2010 of COSMO result files. The fifth tutorial describes how to calculate pK a values Additional information may be found in theCOSMO-RS GUI Reference manualandCOSMO-RS manual

The COSMO-RS GUI module ADFcrs

The COSMO-RS GUI module is:

ADFcrs

This utility ($ADFBIN/adfcrs) enables ADF users to easily select compounds, create COSMO-RS jobs, run the jobs, and visualize the results.

ADF installation

We will assume that you have installed the ADF package on your machines. Depending on your platform, you start the COSMO-RS GUI module in a slightly different way:

UNIX (such as Linux) users

In this tutorial we assume that you have added $ADFBIN to your PATH. We advise you to do this if you have not already done so. If you do not wish to add $ADFBIN to your PATH, you must start the utilities using

$ADFBIN/adfcrs &

instead of just

adfcrs &

On all UNIX platforms, including Mac OS X, the ADF-GUI programs are XWindow programs. Your environment should have been set up correctly to run such programs. In particular, you need to make sure that your DISPLAY environment variable has been set properly.

You can test this easily by starting a simple X program from your shell:

xcalc &

Assuming the xcalc program is in your $PATH, a small window should appear with the image of a calculator. If not, please consult your local system administrator for additional help. Typical problems have to do with your DISPLAY variable, and with security issues when trying to connect to the X server.

3

Windows users

In this tutorial we will assume that you have installed the ADF packaged using the Installer with all default options.

You can start the COSMO-RS GUI (adfcrs) by double-clicking its icon on the desktop.

Macintosh users

Macintosh users have several easy ways of starting the ADF-GUI modules: just like on any other UNIX system (thus, using the command line), or using the ADFLaunch program.

The easiest way is using the 'ADFLaunch' program. When you start it, ADFjobs will be started automatically. Next you can use the SCM menu to start the COSMO-RS module.

4

Tutorials

Tutorial 1: COSMO result files

If you already have COSMO result files for all the compounds that you are interested in you can skip this tutorial, without problems of continuity. For example, ADF has a database of COSMO result files, the COSMO-RS database ADFCRS-2010.

The purpose of this tutorial is to teach you how to make data for a compound using the ADF program such that it can be read by COSMO-RS. COSMO-RS expects so called COSMO result files, which are results of quantum mechanical calculation using COSMO. In ADF such a COSMO result file is called a TAPE21 (.t21) file, or a COSKF (.coskf) file. For example theCOSMO-RS database ADFCRS-2010consists of .coskf files. In other programs such a file can be a .cosmo file. For example, athe.cgnsiu/edt..v-TVtt:ph.wed//ww Databases.htmlfiles can be found, which were made with a different program. Notea database of .cosmo that the optimal COSMO-RS parameters may depend on the program chosen.

Please read through the first ADF-GUI tutorial before starting with this tutorial, seeADF-GUI tutorial. Even better: try using the ADF-GUI yourself, especiallyTutorial 1

Step 1: Start ADFinput

For this tutorial we prefer to work in a separate directory, for example the Tutorial directory, as was explained inADF-GUI Tutorial 1.

You know how to start ADFjobs (in your home directory), and move to the Tutorial directory:

Start adfjobs Click on the Tutorial folder icon

Next start ADFinput using the SCM menu. Notice that currently no job is selected. If a job is selected, the SCM menu will open the selected job, which is not what we want now. You can toggle the selection in ADFjobs using the right mouse button (or control-left). To clear the selection, click anywhere in the search bar on the bottom (except in the input fields).

Make sure no job is selected in ADFjobs. Select theSCM → ADF Inputmenu command.

Step 2: Create the molecule

First we construct a water molecule, and preoptimize its geometry:

Select the O-tool by clicking on the button with the 'O' Click somewhere in the drawing area to create an oxygen atom Select the select-tool by clicking on the button with the arrow Click once in empty space so nothing is selected SelectAtoms → Add Hydrogen Click the optimizer button

Your water molecule should look something like this:

5

Step 3: Optimize the gas phase geometry

The next step is to optimize the geometry using ADF. In this case we will use the Becke-Perdew functional and a TZP basis set, since those are used for the optimization of the COSMO-RS parameters.

Enter a proper title in the Title field (like 'water') SelectPreset → Phase CRS Gas

6

For your information, the proper settings for the gas phase geometry optimization are: The Becke Perdew exchange correlation functional (GGA:BP), use of the scalar relativistic ZORA Hamiltoninan, a TZP small core basis set (for Iodine a TZ2P small core basis set), and an integration accuracy of 6. Like for Iodine for heavy elements a TZ2P small core basis set is recommended.

With the proper options selected, now run ADF:

SelectFile → Run In the file select box, choose a name for your file (for example 'water gasphase' to make a distinction in the _ names of the gas phase molecule and the solvated molecule) and click 'Save'

Now ADF will start automatically, and you can follow the calculation using the logfile that is automatically shown.

Wait until the optimization is ready (should take very little time) Click 'Yes' in the pop-up to read the coordinates from a .t21 file.

Now the geometry of the water molecule is the optimized one.

7

Step 4: Set up the COSMO parameters

First set up the COSMO calculation with the COSMO parameters as they were used in the ADF parametrization of COSMO-RS. The molecule is in a solvent, represented in the COSMO model by a dielectric medium with a dielectric constant. This dielectric constant is infinite in the COSMO-RS model.

Select

Preset → Solvent CRS

Part of the COSMO parameters that are set can be found if one selects the 'Solvation' panel with the pull- down menu on the right side of the window (Click on 'Main Options' and select 'Solvation'). The dielectric constant is infinite if one chooses 'CRS' for the Solvent. The so called 'Klamt' radii are used for the construction of the molecular cavity.

8

Another part of the COSMO parameters that are set can be found if one selects the 'COSMO' panel with the pull-down menu on the right side of the window:

9

10

Step 5: Perform the COSMO calculation and obtain the COSMO result file

For the COSMO-RS calculation it is important that both the energy of the gas phase molecule and the energy of the solvated molecule are known. Also important is to use the same charge and/or spin- polarization in the gas phase molecule as in the solvated molecule. In order to have both values a restart is required with the .t21 file of the gas phase molecule as restart file for the solvated molecule. Note that this is a different procedure than in the ADF2008.01 tutorial.

Select the 'Files (Restart) panel with the pull-down menu on the right ' Click the file select buttun next to 'Restart file', a popup window will appear _ Select water gasphase.t21 (the .t21 file of the gas phase molecule) Click 'Open' in the pop-up

For sake of clarity we will save the COSMO calculation under a different name:

Select the 'Save As..' command from the 'File' menu In the file select box, choose a name for your file (for example 'water') and click 'Save'

With the proper options selected, now run ADF:

SelectFile → Run

Now ADF will start automatically, and you can follow the calculation using the logfile that is automatically shown.

Wait until the optimization is ready (should take very little time) Click 'Yes' in the pop-up to read the coordinates from a .t21 file.

11