Constructing molecules

 

            Chemcraft provides different possibilities to build molecules and change their geometry, which are useful for preparing an initial approximation for computations, and other purposes. In many cases, a molecule can be easily built using standard molecular fragments (see Working with molecular fragments).

            If two atoms are selected, pressing Ctrl+B inserts or removes a bond between them. To alter the type of a bond (e.g. to make a bond dotted), double left-click on it.

            One can modify any geometrical parameter (bond length, bond angle, dihedral) using the textbox at the bottom of the main window. When one selects 2, 3 or 4 atoms, the value of corresponding parameter is shown in the textbox. Attention must be paid to the sequence in which the atoms are selected. If one modifies the value and presses Enter or the "set" button, the positions of atoms are adjusted to the new value. Either the coordinates of last selected atom will change, if the button  is pressed, or the coordinates of first and last selected atom will change symmetrically with the button  pressed. Other atoms bonded to the selected ones will move along with them, so it is often important to insert or remove bonds, before changing a geometrical parameter, via Ctrl+B. Specifically, the coordinates of all atomic groups bonded to last (first) selected atom (i.e. directly bonded, not through intermediate second/third selected atoms when changing angle/dihedral) but not directly bonded to opposite first (last) selected atom, will be changed (the coordinates of these atoms would be translated in parallel with last (first) selected atoms, when a distance is changed, or rotated along second/third selected atom together with last (first) selected atom, when an angle/dihedral is changed). Pressing Ctrl+E moves the focus to the textbox with the value of current geometrical parameter.

            The program allows the coordinates of atoms to be changed by "dragging" them using the mouse. The atoms or fragments are "dragged" in dragging mode toggled by the "Edit/Drag atoms" menu item or the button . Three submodes of the dragging mode can be used:

            Drag individual atoms, : clicked atoms are moved in X or Y directions with the mouse. Pressing Num2/Num8 or Num1/Num3 (while the left mouse button is pressed) moves the atom in Z direction (in parallel with the view orientation);

            Drag fragments, : individual radicals (bonded groups of atoms, enclosed by the clicked atom and not including the largest of these groups, which is considered by the program as the outer molecule) are dragged and rotated, keeping constant the bond length, by which the fragment is connected with outer molecule. Pressing Num2/Num8 moves the fragment in Z direction; pressing Num4/Num6 rotates it along the bond connecting it with outer molecule; Num7/Num9 shortens/lengthens this bond;

            Drag molecules, : whole molecules (bonded groups of atoms connected with clicked atom) are dragged. Pressing Num1-Num9 moves the group in Z direction or rotates it.

            For the last two modes, the bonds in molecule determine the atoms to be dragged together with the clicked atom, so it is often needed to add or remove bonds via Ctrl+B before using these modes.

            A group of atoms can be also rotated along the axis, defined by two selected atoms, via "Edit/Rotate along selected" menu item. This opens a window with a scrollbar, which rotates the atoms bonded with second selected.

            In some cases, it is helpful to perform complex geometry modifications using the Console Editor ("Tools/Console editor" menu item). It provides an iterative algorithm for applying new values for an arbitrary set of geometrical parameters. The values of parameters are entered in text mode (e.g. "r(1-2)=2.1, a(3-2-1)=120,").

            If an undesired change of coordinates is made, Ctrl+Z can be used.

 

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