Built as an educational application, Molecular Geometry can teach you how to identify molecular shapes. The software can also help you learn how to understand interactions and how to predict the shape of a molecule.
Being developed using the Java programming language, Molecular Geometry is a cross-platform utility that can be used on Windows, Mac OS X and Linux.

 

 

 

 

 

 

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Molecular Geometry is a visualization and exploration tool for molecular graphics. It allows the user to set up a molecule, add atoms, energy and charge. Then the user can visualize the molecule, add labels to atoms, save the molecule, set up a new molecule or comment on the current one. You can also change the color of atoms and some other properties.
Then you can print the molecule, save as a png image (chemical or 3D), change the color mode of the background or export as a postscript or pdf file.
Molecular Geometry has several ‘cheat’ functions available to help you. These include:
– Changing any text color to any color you want
– Changing any background color to any color you want
– Changing text font size
– Changing the default text color
– Changing the scale of atoms (text distance)
– Changing the default background color
– Adding atoms from any file type to a molecule
– Adding energy (atom-atom, bond-bond, charge transfer, etc.)
– Adding charge
You can also easily add images to the molecules using an image library.
Molecular Geometry also offers several convenient ‘help’ commands. These include:
– View molecule info for any molecule
– Tells you what atoms there are in the molecule
– Tells you the bond type (single, double, triple, etc.)
– Tells you the bond order (1 to 4)
– Tells you the type of bond (covalent, ionic, etc.)
– Tells you the number of bonds, if applicable (e.g., a radical)
– Tells you the type of charge (positive, negative, zero)
– Tells you the total charge
– Tells you the element, and atom, count (number of bonds to any atom, number of atoms, etc.)
– Tells you the total energy
– Tells you the bond length
– Tells you the bond angle
– Tells you the bond order
– Tells you the bond dissociation energy
– Tells you the bond length
– Tells you the bond dissociation energy
– Tells you the angle between two bonds
– Tells you the angle between two bonds
You can also easily add proteins with their bonding information, which allows you to study the structure and chemical makeup of proteins, including their side chains. Molecular Geometry also contains many fun educational functions such as:

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Molecular Geometry is a Java application written from the ground up to help you with two- and three-dimensional geometry. The program’s interface is modern and professional-looking, and features an easy-to-use drawing board. You can draw molecular shapes using the methods of classical chemistry, thermochemistry or molecular graphics. The software is based on Jmol 3.1, a free Java applet for two- and three-dimensional visualization of molecules.
Molecular Geometry allows you to generate various 2D and 3D molecular models using chemical formulas or structures that have been prepared using the MarvinSketch application.
Molecular Geometry features an intuitive interface that allows you to create, save and delete molecular structures, as well as various geometrical aspects such as symmetry, energy and charge, and calculate different energies (enthalpy, entropy and free energy) related to these molecular structures.
In addition, you can assign partial charges to atoms, calculate dipoles and orientation of molecules, and generate symmetry elements.
Molecular Geometry’s applications list includes an ability to draw and measure molecular shapes, and calculate conformational, spectroscopic and thermochemical properties.
In order to help you to understand interactions between molecules, the program can calculate geometry-dependent thermochemical parameters and create the least energy path between two molecules. The software can also be used to predict the position of atoms within a molecule, and calculate geometry-dependent thermochemical and spectroscopic properties (IR, NMR and fluorescence).
Molecular Geometry runs natively on Windows, Mac OS X and Linux, and its installation packages have been designed to make it easy to install and run the program on those platforms.
Learn More about Molecular Geometry…

EVALUATION

In a word: stinks

ComputerWorld review of Molecular Geometry 1.2.0

SUMMARY

Molecular Geometry is a very simple and basic program that can help you to calculate molecular geometry. The interface is simple, but the list of features is disappointingly limited.

PROS

CONS

No text, images or video tutorials are included, only simple instructions and screenshots.

The problems with the software begin at the first user registration: it is impossible to register due to Microsoft server that is out of service. You can register as a guest or try to use the “instant registration” option, but the software will not work properly.
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Molecular Geometry Free

Since the discovery of the buckminsterfullerene in 1985, a number of researchers have discovered other molecules that have similar shapes to the fullerene, including the buckminsterfullerene-like molecule named C60. Even these molecules are too small to discern. However, there are many molecules much larger than these molecules in biology that have these shapes. In fact, a small fraction of the proteins, polysaccharides, and other biological structures that the owner intends the shape. Some of these other structures are also of use to us in various ways.
Molecular Geometry will help the user by providing a molecular representation of the structure; facilitating you to see how it looks like in 3D. You can also test all the commonly occurring molecular geometry types. The software is available in four different languages: French, English, German and Spanish. The latest update contains a variety of improvements including the demonstration of the Keplerate series. Molecular Geometry is developed using an efficient algorithm for mapping molecular structures.
What are these molecules and why should we care about them? These are questions that will help the user learn why these shapes are important. For instance, the triangulations, which is a series of triangles drawn between every two atoms, are often used in nanoscale science and engineering. It is very important in protein-ligand interactions, where the 3D shape of the protein determines how it interacts with the ligand. This means that it is important to study these shapes which may also help us to understand cancer.
How does it work? Here is a short introduction to how Molecular Geometry works.
Molecular Geometry, like most of the Java games, is an OpenGL application. Java games are possible because of JOGL that is a Java binding to OpenGL. The Java binding to OpenGL uses objects to define the coordinate systems, vectors, matrices and rotations. The abstraction of these objects and the Java binding makes it possible to port Java games to Linux, Mac OS X and Windows.
The following list describe the various objects of the software. The objects are arranged by class. The first 5 classes are:
class MolecularGeometry;
Objects:
Java class: Coords, Vectors, Matrices, Rotation, AtomicJ
Java Class: Shape, Vertex, Atom, Triangle, TriangleList, Polygon
JOGL class: GLU, GLUquadric, GLUquadricView, GLUQuadric, GLUQuad

What’s New In Molecular Geometry?

Molecular Geometry is a molecular modeling and visualization program. Based on Java, it can be run on Windows, Mac, and Linux. The basic principle is a ‘coloring’ scheme depending on certain parameters.
There are a variety of options in order to interpret molecular structures and their shape and provide information about the interactions and chemical reactions of the molecule. The 3D view, 2D view, H-bond, SB-bond, pi-pi interaction, similarity view, energy output view, etc. are available for your convenience.
In the future, additional tools will be added to produce additional reports. For example, protonation, rotamer, charge state and charge distribution.
The aim of Molecular Geometry is not only to help you identify the shape and geometry of the molecule, but also to provide additional information about the molecule and the potential functions.
Molecular Geometry Features:
1. Molecule Structure View
The basic principle is ‘coloring’ the molecular structure depending on certain criteria. You can use a Java-based main program to draw a molecular structure using its ribbon representation.
Note: If you use too many colors on the structure, and the main program cannot display those colors using the given structure, you can use the options in the dialogue box to adjust the colors.
You can clearly identify the shape, size and geometry of the molecular structure. The molecular structure can be displayed from a variety of angles.
2. Shape View
You can clearly visualize the molecular structure, and you can distinguish the hydrogen bond, pi bond and pi bond critical point.
3. Orbit View
If you select a certain portion of the molecule, you can see the charge distribution, H-bond and pi-bond, etc.
4. Energy View
You can view the energy changes of the orbit of the molecule, and you can see the potential energy curve, and the HOMO and LUMO.
5. H-bond View
By double-clicking the H-bond, you can see its effects and the distance, etc.
6. Interaction View
By double-clicking the interaction, you can identify the number of hydrogen bonds, pi-bond, pi-bond critical point, dihedral angle critical point, maximum dihedral angle and dihedral angle (C(60) or C(s)).
7. Similarity View
You can find similar molecules and know which structure is similar to which

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System Requirements:

Minimum:
OS: Windows 7
Processor: Intel Core 2 Duo
Memory: 2 GB
Hard Disk: 3 GB free space
Graphics: NVIDIA GeForce 8600GT / ATI Radeon X1600
Network: Broadband Internet connection
Sound: DirectX 9 compatible sound card (optional)
Additional Notes:
Windows 8 games don’t work under Windows 7. For Windows 8.1 games, make sure you have the latest version of DirectX installed.
Mac OS X: 10.7

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