Application Note. U. Heat of Formation of Ethyl Alcohol and Dimethyl Ether. Introduction

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1 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. You will learn how to Build simple molecules from scratch Build up and work with a library of molecule fragments Work with models of molecules in non-periodic and periodic representations Calculate the heat of formation of molecules In this application note, we show how to build the isomers ethyl alcohol and di-ethyl ether and calculate their respective heats of formation. A separate application note deals with positioning molecules on surfaces and calculating binding energies and related properties:dehydrogenation Energy of Ethyl Alcohol (Ethanol) on a Cu (111) Surface The MolecularBuilder interface offers a range of features like coordinated drawing and translation/rotation of groups of atoms. It also allows building up fragment libraries of molecular building blocks, thus making it easy to assemble larger and more complex molecules and to position molecules with respect to e.g. a surface or an interface. 1. Building ethyl alcohol, C 2 H 6 O In the MEDEA menu click File New Molecule or alternatively press Ctrl-M MEDEA opens a new window displaying the Molecular Builder graphical user interface. a. Constructing the molecule The Molecular Builder uses the concept of active bonds. Active bonds are used to make connections between atoms, using a default bond length given by the covalent radius of an element. For each element the Molecular Builder displays a default number of active bonds, e.g. four for Carbon and two for Oxygen. Note that the number of active bonds (or coordination number) for a given element is not a well defined physical quantity but merely an empiric concept borrowed from chemistry (Lewis structure 1 and electron dot structure). To construct a molecule, select an atom type from the periodic table, choose its connectivity and click on an active bond to form a connection. To build C 2 H 5 OH from scratch, start with Carbon. 1 Lewis structure: see also: Copyright Materials Design, Inc

2 To insert Carbon atoms, select C from the periodic table in the Insertion panel. The default tetrahedral coordination for C is automatically highlighted in the coordination selector on the lower right. Leave this value at its default value 4. Move the mouse cursor into the drawing area on the left Note that the cursor shape changes to the cursor is loaded with the selected element type, indicating that Left-click to deposit a C atom in the drawing area. Note that the cursor remains loaded Move the mouse cursor over one of the active bonds of the C atom (active bonds turn pink when selected) and left-click one more time to add a second C atom. While holding down the left mouse-button you can rotate the newly added atom around the bond. Copyright Materials Design, Inc

3 To undo your last action click Ctrl-Z or the window, to redo an action click the button button on the left hand side of the MEDEA main Next, select O from the periodic table. Note that when selecting O, the coordination selector. Add an O atom to one of the C bonds by highlighting an active bond and left- changes to clicking To add hydrogen to the remaining active (dangling) bonds, select H and drop it atom by atom on each active bond, or simply click Hydrogenate in the lower right to put H atoms on all active bonds at once To rotate, zoom, or translate the whole molecule, hold down the r,z,or t key and move your mouse cursor. To select an atom or a number of atoms, hold down the s key and click on the atoms(s) or hold down the s key, left-click-hold and draw a rectangle to select all atoms within its boundaries. Repeated clicking on an atom in selection mode toggles the selection on and off b. Creating a periodic model Now the next step is to create a periodic boundary box to make it a structure suitable for Vasp. Select the Cell panel to set size and shape of the bounding box: (a, b, c, α, β, γ ). To change the amount of vacuum type in values for (a,b,c) directly, or Compute a cell leaving a gap of Ång. In this example we are planning to compare the energies of two molecules. To minimize numerical errors, we should therefore work with identical box sizes Copyright Materials Design, Inc

4 Check the button Show Cell to visualize the periodic cell. You can right-click the molecule and select All Center to reference point to center the molecule in the cell. In the field for Bounding box cell set box parameters (a,b,c) as (10,10,10) and select Create a periodic copy. Submit a VASP job with atomic relaxation using a single k-point, real-space integration with defaults for all other settings. c. Selecting, deleting multiple atoms, active bonds Back in the Molecular Builder window, change to selection mode by clicking in the MEDEA panel (upper left) or by holding down the s-key. In selection mode, click atom per atom to mark as selected all atoms except for the two C atoms and the H atoms belonging to the CH 3. In selection mode, alternatively to selecting atoms by clicking on them, you can drag open a rectangle using your left mouse button to automatically select all atoms inside. Clicking on a selected atom toggles the selection off. Next, right-click and use Selection Delete selected atoms (Hotkey: Del) from the list of choices. You are left with C-CH 3. Right click the single C atom and select Atom Delete atom only This leaves you with a methyl group CH 3, however as you will notice the remaining C atom preserves its fourth bond as an active bond (dangling bond) Copyright Materials Design, Inc

5 d. Saving structures to the fragment library To save a molecule as a fragment the Molecular Builder requires an active bond to be present. You can also save a complete molecule to disc (File Export) or to MEDEA s internal database (File Save). Here, we have just created a fragment by deleting one of the C atoms and leaving a bond at the other one. To save the methyl group fragment right-click anywhere into the structure and select Save as Fragment from the menu. Select a descriptive name (e.g. the formula unit plus chemical name) and click OK. MEDEA saves the molecule to a temporary database. Note: When saving a fragment, MEDEA saves a bitmap of the structure as-it-is-on-screen along with the structure data. By zooming in on the fragment arranging it in a well-to-lookat position before saving it to the library, you can improve the appeal and readability of the saved system. For later use let s create and save two more fragments, namely those of ethyl alcohol: Replacing a H atom of the methyl group (CH 3 ) Replacing the H atom of the OH group (OH) Right-click anywhere in the structure window and use Save as Fragment to keep it for further use in MEDEA's database. To transfer fragments between computers, use the Insertion panel of the Molecular Builder, click Load fragment Export library to file to save it on disk. Library files can be imported (on a different computer).with Import a library from a file. 2. Building the isomeric di-methyl ether CH 3 OCH 3 Next we will build the isomeric di-methyl ether. In the MEDEA file menu, select New molecule or type Ctrl-M. In the Insertion panel, select Oxygen with default coordination and drop one atom onto the drawing area. Click Load fragment in the Insertion panel, select the methyl group (CH 3 ) and click OK Copyright Materials Design, Inc

6 Move the mouse cursor over each of the two active bonds on O and drop a CH 3 on each of them. Make sure the active bonds are highlighted before you left-click to drop the fragment, otherwise MEDEA will fail to make the connection O-C. To undo an action click Ctrl-Z or the undo button in the MEDEA interface. Again select the box size (a,b,c) to be (10,10,10) as you did for ethyl alcohol and create a periodic model by selecting Create periodic from the MEDEA Edit menu. Submit a VASP atomic relaxation using a single k-point, real-space integration and defaults otherwise Results An atomic relaxation using the VASP parameters Normal precision, Real space integration, 1 k-point, yields the following heats of formation: molecule heat of formation difference Dimethyl ether kj/mol kj/mol Ethyl alcohol kj/mol. 0 kj/mol This indicates ethyl alcohol as more stable than dimethyl ether by ~48 kj/mol. The experimentally found value is~51 kj/mol 2. 2 Reference: NIST Chemistry WebBook, Copyright Materials Design, Inc