Ten simple rules on how to create open access and reproducible molecular simulations of biological systems

Many covalent molecules have central atoms that do not have eight electrons in their Lewis structures. These molecules fall into three categories:

Chemical bonds are complex interactions between two or more atoms or ions, which reduce the potential energy of the molecule. Gilbert N. Lewis developed a model called the Lewis model that simplified the depiction of chemical bond formation and provided straightforward explanations for the chemical bonds seen in most common compounds.

To determine the electron configuration for any particular atom, we can build the structures in the order of atomic numbers. Beginning with hydrogen, and continuing across the periods of the periodic table, we add one proton at a time to the nucleus and one electron to the proper subshell until we have described the electron configurations of all the elements. This procedure is called the aufbau principle, from the German word aufbau (“to build up”). Each added electron occupies the...

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

Molecular Orbital Energy Diagrams

The quotient rule is a fundamental differentiation technique in calculus used to differentiate functions expressed as a ratio of two differentiable functions. Given a function of the form:Where g(x) and h(x) are both differentiable and h(x) ≠ 0, the derivative of f(x) is given by:Example:The quotient rule is beneficial when differentiating rational functions, trigonometric ratios, and exponential functions. For example, given:applying the quotient rule,This rule is essential in solving...