Computer Technology in Medical Field
Computational Chemistry: Conformational Analysis of Ethane and Butane
Objectives: To visualize molecules in 3-dimensions. To learn how to use the Spartan ES software. To compute and graph the relative conformational energies of ethane and butane.
Background:
One of the most successful theories of the 20th century is quantum mechanics, also called wave mechanics. The idea that energy in atoms occurs in discrete bundles is contrary to our everyday notion that energy flows smoothly into or out of a reaction. But on the atomic and molecular scale, our everyday notions must be set aside. Likewise, the notion that matter is composed of solid particles must give way to the idea that electrons and atoms have wave-like properties, and that the wavelength associated with the particle depends on the particle’s momentum. Describing the interactions of the waves corresponding to individual electrons is at the heart of molecular wave mechanics. When the electron waves in a region of the molecule overlap in a constructive way, like water waves reinforcing each other, there is greater likelihood of finding the electrons in that region.
The challenge is to describe this wavelike behavior in enough mathematical detail that we can accurately predict important features of the molecule such as bond lengths, bond energies, and force constants. For the hydrogen atom, the mathematical description of the electron can be written exactly. You have seen the wavelike pictures of the electron in the H atom - the s, p, d, and f orbitals. For larger atoms (and molecules), the problem is so complicated that it cannot be solved. Approximations must be used. Years of research have shown that we need to retain the approximate 3-dimensional shapes of the orbitals, but that we can simplify considerably how we describe the wavelike behavior of the electron with respect to distance from the nucleus.
Spartan is a computer program that uses the atomic orbitals on the individual atoms to
Objectives: To visualize molecules in 3-dimensions. To learn how to use the Spartan ES software. To compute and graph the relative conformational energies of ethane and butane.
Background:
One of the most successful theories of the 20th century is quantum mechanics, also called wave mechanics. The idea that energy in atoms occurs in discrete bundles is contrary to our everyday notion that energy flows smoothly into or out of a reaction. But on the atomic and molecular scale, our everyday notions must be set aside. Likewise, the notion that matter is composed of solid particles must give way to the idea that electrons and atoms have wave-like properties, and that the wavelength associated with the particle depends on the particle’s momentum. Describing the interactions of the waves corresponding to individual electrons is at the heart of molecular wave mechanics. When the electron waves in a region of the molecule overlap in a constructive way, like water waves reinforcing each other, there is greater likelihood of finding the electrons in that region.
The challenge is to describe this wavelike behavior in enough mathematical detail that we can accurately predict important features of the molecule such as bond lengths, bond energies, and force constants. For the hydrogen atom, the mathematical description of the electron can be written exactly. You have seen the wavelike pictures of the electron in the H atom - the s, p, d, and f orbitals. For larger atoms (and molecules), the problem is so complicated that it cannot be solved. Approximations must be used. Years of research have shown that we need to retain the approximate 3-dimensional shapes of the orbitals, but that we can simplify considerably how we describe the wavelike behavior of the electron with respect to distance from the nucleus.
Spartan is a computer program that uses the atomic orbitals on the individual atoms to