Zoom: Size: Wireframe:

Select Molecule options

These options may allow selection of the entire molecule, subcomponent molecules (for example protein vs nucleic acid), or smaller molecular components (cofactors, carbohydrates, specific nitrogenous bases or amino acids, etc) of the model presented in the Jmol window.

Selecting a molecule so that it’s name heads the menu allows alteration of its appearance in the model.

A molecule can be hidden or revealed using the adjoining checkbox. Hiding a molecule will hide all components (atoms, bonds, ribbon, etc.) of the model associated with that molecule.

Display options

Display options determine how the selected molecule will be rendered in the model. The model may include atoms, bonds, a ribbon, trace, etc, which can be individually sized using the ‘Size’ buttons. The adjoining checkboxes can be used to hide or make visible different model components.

Atoms: Atoms can be rendered as solid spheres with a uniform radius in Angstroms, which together with bonds comprise a traditional ‘ball and stick’ projection. This is normally the default view. Note about hydrogen atoms: some models show hydrogen atoms but others do not.

vdW checkbox: toggles rendering of atoms between uniform diameters and percentage of the van der Waals radius of each element. The van der Waals Radius of an atom is the calculated radius when it is adjacent to but not bonded to another atom. Since the van der Waals radius of an element is related to the size of its electron cloud, elements with greater mass will have larger van der Waals radii.

Dots: This projects an array of small dots around the surface of atoms. Dots are a useful way to show a molecular surface while not obscuring other aspects of the molecular structure, such as a ball and stick rendering. If vdW is checked, the dots are drawn as a percent of the van der Waals radius.

Bonds: Covalent bonds are generally drawn as rods between the atoms. In some models single, double and triple bonds are distinguished (but this does not occur in all models).

H-bonds: The position of hydrogen bonds is calculated by the Jmol applet. This is performed between N-H and C-O groups of proteins and between nitrogenous bases of nucleic acids. Thus, not all hydrogen bonds may be rendered in a model.

Ribbon: A ribbon-like feature that follows the backbone of DNA and proteins. For nucleic acids, a ribbon will follow the sugar-phosphate linkages, and for proteins it follows the path of peptide bonds and alpha carbons. The flattened appearance of the ribbon highlights secondary structural features, such as the alpha-helices and beta-sheets of a protein.

Trace: Like a ribbon, a Trace follows the molecular backbone, but is rope-like in appearance. A Trace shows the path of the backbone while allowing other structural features to be emphasized.

IsoSurface: IsoSurface projects a surface to a molecule as it would appear to water molecules rolling along the perimeter. This is also referred to as the Sovent-excluded or Connolly surface. Follow this link for a more complete description of the rendering of molecular surfaces.

Color by options

Atoms, Ribbons and Traces can be colored to highlight structural features. Follow this link for a more complete description of colors.

Element: Atoms will be colored according to element type. The colors of the most common elements are:

H C N O P S Fe

1o Structure: different types of amino acids and nucleotides are given a unique color (according to the Jmol ‘shapely’ color scheme).

2o Structure: This differentiates regions of protein secondary structure:

α-helix β-sheet

4o Structure: This gives a different color to each peptide subunit of a multi-subunit protein and to each strand of a nucleic acid.



Molecular Bonds

Examine the following models to explore different types of molecular bonds. Change the appearance of the models as you wish. Instructions for rotating, moving and zooming the models can be found on the Move? link.

Properties of Some Biologically Important Atoms
& color
# of
1Hydrogen - H112.20
6Carbon - C442.55
7Nitrogen - N533.04
8Oxygen - O623.44
11Sodium - Na110.93
12Magnesium - Mg221.31
15Phosphorus - P352.19
16Sulfur - S622.58
17Chlorine - Cl713.16
19Potassium - K110.82
20Calcium - Ca221.00
26Iron - Fe531.83
1 Number of electrons in outer shell
2Most common number of bonds formed
3 'Χ' = Electronegativity -- relative tendency to attract electrons

1. Covalent Bonds form the sturdy structural backbone of biological molecules and exist when atoms share electrons.

A. Single, double and triple covalent bonds form when atoms share one, two or three pairs of electrons in order to fill their outer valence shells, as shown in the diagrams to the right. Click here to view ethanol, a simple organic molecule in which the atoms are all joined by single bonds. Click here to view urea, a molecule used by the body to dispose of nitrogen waste, which contains a double bond between the carbon and oxygen. A triple bond forms when atoms share three electrons, as shown here in cyanide, the toxin. Triple bonds are rare because they are quite reactive and unstable.

Notice that each type of atom forms as many bonds as needed to complete an octet of electrons in it's outer shell. For example, the carbon of the cyanide molecule has four electrons in its valence shell and needs to form four bonds (shared pairs of electrons) to have a full octet. The carbon does this by forming three bonds with the nitrogen and one bond with the hydrogen. The nitrogen also needs to have an octet, but it has five electrons of its own in its outer shell, so it only needs to form three bonds to bring it up to an octet.

B. A Polar Covalent Bond has an asymmetric distribution of electrons because some atoms tend to attract electrons more strongly than others; a property called electronegativity, and designated by the Greek letter Chi (Χ). When the difference in electronegativity lies between 0.4 and 1.7, as in bonds between C - O, O - H, P - O and N - H, the more electronegative atom assumes a partial negative (δ-) charge, leaving the other atom with a partial positive (δ+) charge. The polarity (or 'dipole') of a bond is often diagrammed as shown in the figure to the right. Click on the following buttons to diagram the polar bonds in each of the molecules. EthanolUreaCyanide

2. Molecules can be non-polar, polar, or amphipathic.

A. Nonpolar Molecules have no significant polarity. For example, hydrocarbons such as Hexane possess only carbon and hydrogen atoms that do not form significantly polar bonds. Sometimes the orientation of polar bonds may cancel out polarity for the molecule overall. Click here to show diethyl ether, which has polar bonds in opposite orientations. Molecules classified are lipds are also largely non-polar; for example,steroidal hormones can possess several polar bonds but still be largely non-polar.

B. Amphipatic molecules are largely non-polar but possess a strongly polar region. Click here to show caproic acid (a smelly component of goats), which has a polar carboxyl (acidic) group at one end and a non-polar region at the other. Click here to show a steroidal molecule linked to a highly polar sulfate (SO4) group, creating an amphipathic molecule.

C. Polar Molecules have a preponderance of polar bonds that imparts a net overall polarity upon the molecule. Most biomolecules are polar, and thereby hydrophilic, able to dissolve in the cell's water environment. Click here to show acetic acid and its polar carboxyl group. Carbohydrates, such as glucose, are also hydrophillic and possess many polar bonds.

The polar groups of molecules often participate in interactions between molecules, such as through ionic or hydrogen bonds.

3. Ionic bonds form between atoms or molecules of different charge.

A. Ions are atoms or molecules that have a stable net charge. Negatively charged ions are called anions and positively charged ions are called cations. As shown in the two diagrams, in order to establish a more stable, full octet of electrons in their outer valence shell, atoms such as Na, Ca and K tend to donate electrons, while other atoms such as Cl and Br accept electrons. Typically electrons are passed between atoms that have large differences in their electronegativity( for example from Na (0.93) to Cl (3.16).

Organic molecules can become charged also. Organic acids, such as lactic acid, ionize by releasing a hydrogen atom; other molecules may be bound to a negatively charged group such as SO4 or PO4, such as in glucose-1-phosphate.

B. An Ionic Bond is created by the electrostatic attraction between a positively charged ion (cation), such as Na+, K+ or Ca2+, and a negatively charged ion (anion), such as Cl-, Br- or lactate-. Click here for a projection of the ionic attraction between K- and Na+, and here to see the ionic bonding of Na+ to lactate.

4. Hydrogen bonds are similar to ionic bonds, except that the positively charged ion is always a hydrogen.

In biological systems, hydrogen atoms that have a partial positive charge may interact with neighboring oxygen or nitrogen atoms that carry a partial negative charge (δ-). For example, the DNA base pairs are held together by hydrogen bonds. In this Adenine-Thymine base pair the hydrogen bonds between the bases are colored magenta. While hydrogen bonds are relatively weak (less than most types of ionic bonds), their combined effect can be significant. Hydrogen bonds between base pairs hold together the two stands of the DNA double helix. (Note: the H-bonds in this model incorrectly extend beyond the hydrogen atoms -- zoom in to see this.)

Hydrogen bonds also help to stabilize the 3-D structure of proteins, as shown in this model of the enzymelysozyme. Instead of showing the individual amino acids, this model displays a ribbon that follows the path of the amino acid chain within the protein and the position of the hydrogen bonds, colored magenta. Notice how the hydrogen bonds help to stabilize the folding of the peptide.

Hydrogen bonds also significantly influence the properties of water and substances dissolved in it. Click here to see a cluster of water molecules with intramolecular hydrogen bonds. Water molecules could also form hydrogen bonds to polar compounds, helping the compound to dissolve in the water.

5. Van der Waals forces are a weak form of intermolecular molecular attraction.

London dispersion force is a type of Van der Waals attraction caused by the uneven distribution of electron density across an atom's electron orbitals. This creates partial negative (δ-) and partial positive (δ+) charges on opposite sides of an atom that cause weak attraction between neighboring atoms. Within an atom, the electron density is continuously shifting; however, since neighboring atoms influence each other, their δ- and δ+ change in synchrony, and opposing δ charges maintain a slight attraction between the atoms, as illustrated in this animation:

In biological systems Van der Waals attraction is most important among uncharged molecules, such as hydrocarbons, lipids and non-polar amino acids.

For example, these forces strongly influence the properties of biological membranes. This model shows part of a Phospholipid membrane displaying the closely arrayed phosopholipid molecules in a slice of the membrane bilayer. The center region of the bilayer consists of hydrophobic fatty acids. Click here to zoom in and highlight the Van der Waals bonding. Although Van der Waals bonds individually are weak, their abundance has significant affect on the movement (fluidity) of the phospholipids in the membrane.

Dept of Biology & Environmental Science

Steven R. Spilatro
© 2008

Test Your Knowledge of Molecular Bonding

Answer the following questions and perform the following activities. Change the appearance of the models as you wish to facilitate answering questions.

Name: _______________________

Date: _______________________

Results for Molecular Bonding Inquiry Activities

1. Identify the properties of different types of molecular bonds.

Match each of these bond types
Single Covalent
Double Covalent
Triple Covalent
Van der Waals
With the correct description given below:
Atoms share 3 pairs of electrons
Attraction between atoms carrying full charges
Atoms share 2 pairs of electrons
Atoms involved carry partial charges
Atoms involved have uneven electron density
Atoms share a pair of electrons

Attempts: Correct:

2. In the following molecules identify the types of atoms and bonds that are present.

Na-K Glutamate, an amino acid.
Nereistoxin-dicyanate, an insecticide.
Keratan sulfate, a component of the extracellular matrix of cartilage and the cornea of the eye.

How many of each of these atoms are present in this molecule? (Press enter to record your answer.)
Hydrogen: Carbon: Oxygen:
Nitrogen: Sulfur: Phosphorus:
How many of each of these bond types are present in this molecule?
Double: Triple: Ionic:

Attempts: Correct:

3. Identify the positions of double and triple bonds in the following models.

a. Click here and then in the spaces provided, type in the number of covalent bonds each of the following atoms should form. (Press enter to record your answer.)
Atoms most commonly forming covalent bonds
# of
1Hydrogen - H1
6Carbon - C4
7Nitrogen - N5
8Oxygen - O6
15Phosphorus - P3
16Sulfur - S6

b. As presented, all of the bonds of the following molecules are shown as single covalent bonds. Select "Add double" or "Add triple" and then, considering the number of bonds each atom should form, click on the bonds that should be double or triple covalent bonds.

2-propynyl-thiocyanate (requires 2 double and 1 triple bond)
Dodecenyne (requires 1 double and 1 triple bond)
Aminomethyl-thiocyanate (requires 1 triple bond)

Add double Add triple

Attempts: Correct:

4. Identify the polar and nonpolar characteristics each of these molecules.

Select each molecule and change its appearance to better display the molecular structure.

Hexanol Isocitrate Serine Alanine Butane

a. Is this molecule polar, largely polar, largely non-polar or non-polar.

Largely Polar
Largely Non-polar Non-polar

b. If the molecule is 'largely polar', click on a bond in the non-polar region of the molecule. If the molecule is 'largely non-polar', click on a bond in the polar region of the molecule.

Attempts: Correct:

5. How are these molecules linked togther?

Examine the following molecules and determine if they would be attracted by ionic bonds, hydrogen bonds or Van der Waals attraction.

Fatty acid and cholesterol
Nitrate in water. What type of bonds occur between these nitrate and water molecules?
Monsodium glutamate. What links the Na and glutamate in the this flavor enhancer?
Base Pair What type of bond links the two bases from a DNA molecule?

Hydrogen bonds
Ionic bonds Van der Waals attraction

Attempts: Correct: