Draw potential energy surfaces using gaussian software

#Draw potential energy surfaces using gaussian software code#

One way to define such a path unambiguously is to descend into both valleys from the + pass making a 90В° angle with every contour as it is crossed. Obviously there would be many other paths that would pass through the same + point, but this one seems as good as any for a start. This plot shows the minimum amount of energy that would be required to get from one valley to the other across the pass marked by +. Slicing out a thin section of the PES along the curved trajectory of the previous figure and flattening it to look at the potential energy profile would yield the ' Reaction Coordinate Profile' below. In this plot a single point denotes the position of all atoms. Heller's plot used a separate point for each atom. Note how different this trajectory plot is from the trajectory plot of Heller. The red path is thus a trajectory for the reaction A + BC -> AB + C. From this point on the C atom flies away as A finishes bonding to B. As A gets close to BC, the BC bond begins to stretch until at the pass ( +), d AB = d BC. d AB shrinks from a great distance while d BC stays at the bonding distance for the BC molecule). In fact one can use motion of a single ball on the potential energy surface to show motion of two atoms (changes of both d AB and d BC), as shown in the next figureДЄt first motion of a ball along the red line in this figure corresponds to A approaching BC ( i.e. The only difference between this motion and the one in the first two-dimensional plot is that now it is understood that C is at a given substantial distance from B.

The double-headed violet arrow shows the path of the ball rolling back and forth to display vibration of AB. Slicing this three dimensional PES along the horizontal red line and folding the top section up and back gives a profile (at the top) that is exactly the two-dimensional plot of potential energy for stretching of the AB molecule that was shown at the top of this page. When both d AB and d BCare long (top right) one has three separate atoms at an energy that ceases to depend on further increase in these distances.ДЄt the lower right is a dark valley corresponding to a BC molecule with the A atom far away (BC is short and AB is long).ДЄt the upper left is the corresponding valley for an AB molecule with the C atom far away. There are two valleys meeting at a pass (denoted by the +) with steep cliffs along the bottom and left edges and a plateau at the top right. One could imagine this plot as a topographic map with altitude corresponding to potential energy. (Allowing the molecule to bend at B would require a third geometric dimension and make plotting difficult.)

#Draw potential energy surfaces using gaussian software code#

One can include a third dimension and go from a Potential Energy line to a Potential Energy Surface (PES), by using contours and/or colors to code the Potential Energy as a function of two geometric variables.ДЇor example, the plot to the right shows the Potential Energy for a LINEAR triatomic molecule A-B-C, with darker colors corresponding to lower energies. Motion of the ball can be used to visualize the vibration of the diatomic molecule as the bond stretches and shrinks interconverting potential and kinetic energy. When the ball reaches the bottom of the violet curve, the potential energy has been converted into kinetic energy. The violet circle could be thought of as a ball poised to roll back and forth between the two stationary positions in which all of its energy is potential energy. The red line on this graph is a crude version of such a potential energy curve (the Morse potential) for a bond that can break. This would be hard to graph on two dimensional paper.Д«ut if one is not interested in motion of the molecule as a whole, nor in its rotation, it is easy to draw on paper an explicit graph to show the potential energy ( PE) of the molecule as a function of the distance between the two atoms d AB. PotEnergySurf Potential Energy Surfaces for Structureand DynamicsДЇully specifying the location of a diatomic molecule, AB, would require specifying six numbers, the x, y, and z coordinates of each of its atoms.