Taking A Closer Look at Molecular Modeling

This guide is for medical billing and coding.

Matter is made up of molecules arranged in order to have the composition and the appearance that one sees in any physical item. You may be wondering why such specific arrangement will yield certain characteristics. Many scientists have asked that same question, and they have tried to explain the factors that determine how a substance is constructed. By understanding these factors, representations have been made and theories have been produced in order to explain and define the molecular properties of a substance.

Molecular modeling has been a way of understanding matter by looking into its molecules and representing them through structures and images that will allow people to observe the motion of molecules. This visual representation has been a revolutionary means in determining the properties of certain molecules or compounds. Before delving into that, though, an understanding of the nature of the bonds and the concepts behind this must be considered before undergoing the simulation process. The molecule is a very complex thing that needs understanding. The motion undergone by the electrons can really give significance to the property of the molecule. By representing these motions through the forces and concepts that surround them, the properties associated with the molecule can be understood better.

Lewis Structures

Named after Gilbert Newton Lewis, who pioneered this phenomenon, the Lewis structure is a means of representing the molecules in the form of valence electrons of atoms bonded with others. By representing the atoms through symbols, the bonds are representing initially by dots that signify the sharing of electrons. These are distributed among atoms based on the octet rule that all atoms must have eight electrons in order to be stable. In order to determine the appropriate structure, the least electronegative component of a compound is usually the central atom, and the labeling works from there. This is the basis of organic compounds with Carbon as the central atom and this is helpful in determining the nature of the bonds of compounds.

Formal Charge

Since atoms consist of particles known as electrons, protons, and neutrons, the abundance of electrons and protons will determine the charge of the atom. A charged atom, otherwise known as an ion, has an imbalance of proton and electron count. In molecules, this will determine the nature of the molecule in respect to the ionic bonding with another molecule. It can be calculated by isolating the corresponding elements of the molecule. Then by following the octet rule, the respective charges can be added to get the overall formal charge of the molecule. This is important in determining the behavior of the molecule as it reacts because of the changes undergone. As the electrons give the properties of an element, it would work in line with the properties of the molecules.

Resonance Structures

Some molecules go passed the conventional sharing of electrons in order to attain a more stable configuration. The Lewis structures opts to show the most stable form of a molecule in terms of electron distribution. However, the localized positions of the electrons may be contrary to those presented in observations. The electrons are complexly distributed and because of this, they form resonance and an increased stability of the molecule. These structures are mainly important for their properties in reactivity. If a molecule acting as a reactant were to be resonantly stabilized, reactions undergone by this molecule would be less likely favored. In products that are resonantly stabilized, reactions that produce this product are favored. An application is found in benzene rings containing three alternating double bonds with a significant decrease in reactivity to undergo additional reactions.

Valence Shell Electron Repulsion Theory

Otherwise known as the VSEPR Theory, this states that for an arrangement of electrons in a molecule, the most ideal arrangement is where the electrons are at a minimal repulsion distance from each other. This gives a molecule a certain geometric shape depending on the electron-groups which are the electron pairs found about the central atom of a molecule. The nature of the electrons gives a certain orientation to the molecule and this gives people an idea of the shape of the molecule. This has its roots on the Lewis structure which gives the number of electron pairs. Examples of the geometry that can be formed are linear with two electron groups, trigonal planar with three, and so on as the electron-groups increase.

Bond and Molecular Polarity

In determining the physical properties, such as solubility or melting points, polarity is defined to be how the electrons are shared in a given atom of molecule. In a given covalent bond between elements, if the electrons are equally shared between the regions surrounding the nucleus, polarity is said to be neutral, and as a result the compound becomes non-polar. In other cases, the regions where the electrons travel around would be that around the nucleus of one of the elements of the bond. This forms an unequal sharing of electrons and the compounds are said to be polar. An example of this is solubility where polar solvents have been shown to dissolve polar solutes, and the same is true regarding non-polar solvents and solutes. Molecular polarity is the polarity shared by the totality of the molecules and its definition is comparable to that of bond polarity.

Intermolecular Forces

After understanding how the molecules are arranged, the forces in between them are very important considerations in the physical property of a certain molecule or substance. Intermolecular forces or van der Waals forces are weaker than covalent and ionic bonded forces but they are significant because they indicate the phase of a certain object and they give significance to the melting point, boiling point, solubility, and other physical attributes of a substance. The stronger the intermolecular forces are, the closer the state of the substance is to resembling a solid. Van der Waals forces and some sub-divisions are: dipole-dipole interaction and London dispersion forces. Dipole-dipole interaction is prevalent in most polar covalent molecules. Since there is the presence of charge on both ends of the pole, these interactions are common in molecules such as ammonia and hydrochloric acid. London dispersion forces occur between molecules that are non-polar such as gases like hydrogen, oxygen, or nitrogen. Another name of these forces is the induced-dipole – induced-dipole forces. Known to be the weakest intermolecular forces since gases contain almost no polarity, the molecule may be induced into being a temporary dipole which is responsible for gases to have a minimal form of attraction.