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written by Mark Bishop
This web page contains a large set of three-dimensional molecular models, which can be rotated and enlarged by the user. Included are models of carbon in three forms, 8 metals, 6 non-metals, hydrocarbons, tetrahedrals, acids, alcohols, esters, ethers, proteins, organic structures, saccharides, and more. By using the mouse to rotate images, students can readily see the molecular geometry in the positions of the constituent atoms. Right click to zoom up to 800%, view element symbols and atomic numbers, measure the structure, or highlight the bonds in a customized color choice.  

Editor's Note: Be sure not to miss the additional materials in this large collection. Author Mark Bishop also created two textbooks in introductory chemistry (available in free digital format), Power Point presentations for teachers, tutorials, student guides, and more.
Subjects Levels Resource Types
General Physics
- Properties of Matter
Modern Physics
- Atomic Physics
= Atomic Models
Other Sciences
- Chemistry
- High School
- Middle School
- Informal Education
- Instructional Material
= Activity
= Model
- Audio/Visual
= Illustration
Appropriate Courses Categories Ratings
- Physical Science
- Physics First
- Conceptual Physics
- Algebra-based Physics
- AP Physics
- Activity
- New teachers
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Intended Users:
Access Rights:
Free access and
Available for purchase
Digital versions of textbook are freely viewable; CD and hard-copy versions are available at a cost.
© 2010 Mark Bishop
3D, atoms, matter, molecular chains, molecular models, molecular structure, molecules, states of matter
Record Cloner:
Metadata instance created May 2, 2011 by Caroline Hall
Record Updated:
October 3, 2013 by Caroline Hall

AAAS Benchmark Alignments (2008 Version)

4. The Physical Setting

4D. The Structure of Matter
  • 6-8: 4D/M1a. All matter is made up of atoms, which are far too small to see directly through a microscope.
  • 6-8: 4D/M1b. The atoms of any element are like other atoms of the same element, but are different from the atoms of other elements.
  • 6-8: 4D/M1cd. Atoms may link together in well-defined molecules, or may be packed together in crystal patterns. Different arrangements of atoms into groups compose all substances and determine the characteristic properties of substances.
  • 9-12: 4D/H7b. An enormous variety of biological, chemical, and physical phenomena can be explained by changes in the arrangement and motion of atoms and molecules.
  • 9-12: 4D/H8. The configuration of atoms in a molecule determines the molecule's properties. Shapes are particularly important in how large molecules interact with others.

11. Common Themes

11B. Models
  • 6-8: 11B/M1. Models are often used to think about processes that happen too slowly, too quickly, or on too small a scale to observe directly. They are also used for processes that are too vast, too complex, or too dangerous to study.
11D. Scale
  • 6-8: 11D/M3. Natural phenomena often involve sizes, durations, and speeds that are extremely small or extremely large. These phenomena may be difficult to appreciate because they involve magnitudes far outside human experience.

12. Habits of Mind

12C. Manipulation and Observation
  • 6-8: 12C/M3. Make accurate measurements of length, volume, weight, elapsed time, rates, and temperature by using appropriate devices.

Next Generation Science Standards

Matter and Its Interactions (MS-PS1)

Students who demonstrate understanding can: (6-8)
  • Develop models to describe the atomic composition of simple molecules and extended structures. (MS-PS1-1)

Disciplinary Core Ideas (K-12)

Structure and Properties of Matter (PS1.A)
  • Substances are made from different types of atoms, which combine with one another in various ways. Atoms form molecules that range in size from two to thousands of atoms. (6-8)
Types of Interactions (PS2.B)
  • Attraction and repulsion between electric charges at the atomic scale explain the structure, properties, and transformations of matter, as well as the contact forces between material objects. (9-12)

Crosscutting Concepts (K-12)

Patterns (K-12)
  • Macroscopic patterns are related to the nature of microscopic and atomic-level structure. (6-8)
  • Graphs and charts can be used to identify patterns in data. (6-8)
  • Different patterns may be observed at each of the scales at which a system is studied and can provide evidence for causality in explanations of phenomena. (9-12)
Scale, Proportion, and Quantity (3-12)
  • Time, space, and energy phenomena can be observed at various scales using models to study systems that are too large or too small. (6-8)
  • Using the concept of orders of magnitude allows one to understand how a model at one scale relates to a model at another scale. (9-12)
Structure and Function (K-12)
  • Complex and microscopic structures and systems can be visualized, modeled, and used to describe how their function depends on the shapes, composition, and relationships among its parts, therefore complex natural structures/systems can be analyzed to determine how they function. (6-8)

Common Core State Standards for Mathematics Alignments

Standards for Mathematical Practice (K-12)

MP.7 Look for and make use of structure.

High School — Geometry (9-12)

Geometric Measurement and Dimension (9-12)
  • G-GMD.4 Identify the shapes of two-dimensional cross-sections of three-dimensional objects, and identify three-dimensional objects generated by rotations of two-dimensional objects.
Modeling with Geometry (9-12)
  • G-MG.1 Use geometric shapes, their measures, and their properties to describe objects (e.g., modeling a tree trunk or a human torso as a cylinder).?
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Record Link
AIP Format
M. Bishop, (2010), WWW Document, (http://preparatorychemistry.com/Bishop_Molecules.htm).
M. Bishop, An Introduction to Chemistry: Molecular Structures (2010), <http://preparatorychemistry.com/Bishop_Molecules.htm>.
APA Format
Bishop, M. (2010). An Introduction to Chemistry: Molecular Structures. Retrieved August 1, 2014, from http://preparatorychemistry.com/Bishop_Molecules.htm
Chicago Format
Bishop, Mark. An Introduction to Chemistry: Molecular Structures. 2010. http://preparatorychemistry.com/Bishop_Molecules.htm (accessed 1 August 2014).
MLA Format
Bishop, Mark. An Introduction to Chemistry: Molecular Structures. 2010. 1 Aug. 2014 <http://preparatorychemistry.com/Bishop_Molecules.htm>.
BibTeX Export Format
@misc{ Author = "Mark Bishop", Title = {An Introduction to Chemistry: Molecular Structures}, Volume = {2014}, Number = {1 August 2014}, Year = {2010} }
Refer Export Format

%A Mark Bishop
%T An Introduction to Chemistry: Molecular Structures
%D 2010
%U http://preparatorychemistry.com/Bishop_Molecules.htm
%O text/html

EndNote Export Format

%0 Electronic Source
%A Bishop, Mark
%D 2010
%T An Introduction to Chemistry: Molecular Structures
%V 2014
%N 1 August 2014
%9 text/html
%U http://preparatorychemistry.com/Bishop_Molecules.htm

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An Introduction to Chemistry: Molecular Structures:

Same topic as Concord Consortium: Intermolecular Attractions

This simulation-based model allows deep exploration of the factors that affect polar and non-polar covalent bonding.

relation by Caroline Hall

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