In the field of chemistry, most especially for beginner courses, being able to visualize the three dimensional image of a given molecule or atom is an extremely helpful skill that may not be completely intuitive to everyone. Being able to visualize the molecules and atoms that are presented is extremely helpful when taking into considerations IMF’s (Inter molecular forces) which determine almost all known physical properties, and the number and type of bond between atoms.
So to start the basics must be observed, being able to draw the Lewis Dot structure for any given molecule. As a frame of reference you should be able to draw the Lewis Dot structure for the basic molecule of Ethane (C2H6). If you can’t, I advise going over how to draw the structures using any review material.
Moving on to the actual visualization of the three dimensional model, you must keep in mind that each atom is surrounded by electrons that contribute to creating the “electron cloud” which is essentially a diagram or visual representation of the most likely places the electrons would be. Because each atom contains its own electron cloud, and similarly charged particles repel each other, the cloud for each atom will be as far away from all the electron clouds as possible. For example if you have a simple Methane (CH4), the initial reaction would be to imagine the structure exactly as you see it, in two dimensions.
However when you take into account that the distance between two H+ atoms on opposite ends, if they were distributed on the same plane, would be a full 180° as opposed to a 90° distance between any adjacent H+ atom. In order to rectify this discrepancy, the distance between any given atom should be about 108°, resulting in a structure that looks like this:
Now that a general idea for the workings of 3-D visualization is intact, there is one small discrepancy to take into account. When a molecule has a lone pair of electrons such as in H2O, the distance between the two H+ atoms is slightly smaller than 108°, coming in at 104°. While it may not seem like a large difference, it is important to understand why this happens. When lone pairs are present in a molecule they have a higher negative density and are found to be closer to the atomic nucleus therefore exert more force on the other atoms.
In closing, learning how to visualize a three dimensional model is not something that can be instantly done, practice and application is required. Attempt to find examples of chemical molecules in a textbook and practice visualizing the 3-D structure, once you have done so go to Google and check to see if you are correct. After a while this should soon become second nature and you will have gained a valuable new skill to aid you in the field of Chemistry!