6 Best Free Molecular Modeling Software For Windows

Here is a list of Best Free Molecular Modeling Software For Windows. These software let you draw the molecular structures of different chemical compounds. Simply select an element from the periodic table and place it on the provided workspace. You can add hydrogen atoms to your model in just a single click or one by one manually. You can also change the order of atomic bonds as single, double, triple, hybrid, etc.

In these molecular modeling software, you will find different styles to represent a chemical structure. These styles include ball and stick, wireframe, wireframe CPK, CPK, stick, constellations, pipes, CPK Spacefill, BallCylinder Low, BallCylinder Medium, etc. In a molecular model, you can also change the color and radius of atoms. Besides this, you can also add a label to the molecular model.

For convenience, some chemical groups and structures are also provided. Alcohols, aldehydes, alkanes, alkenes, alkynes, amides, amino acids, carbohydrates, carboxylic acids, ethers, sulfoxides, etc. are some of these chemical structures. You can use them directly in your molecular models. In addition to this, structures of DNA and RNA are also available in some molecular modeling software.

In most of these software, you will be able to perform Gaussian Calculations, Energy Calculations, Optimize the Geometry of a chemical model, Electronic Spectrum Calculations, Dock Base Calculations, etc.

You will also find a software which displays the temperature, pressure, dipole moment, quadrupole moment, energy, intermolecular energy, gradient, etc. of a molecule.

After creating a chemical structure, you can save it in different formats, like PDF, SVG, BMP, JPG, PNG, POV-Ray, etc.

My favorite molecular modeling software:

Avogadro is my favorite molecular modeling software. It offers a hassle-free user interface which lets you draw different chemical structures easily. You can also change the color of an atom, order of bonds, etc. Moreover, there are different styles to represent a chemical structure. Plus, it supports multiple formats to export/save a molecular model, like SDF, SD, CHT, DMOL, GAM, INP, GAMIN, GAMOUT, PDF, SVG, BMP, JPG, PNG, POV-Ray, etc. You can also animate your designed model in Avogadro.

You may also like some best free Chemistry Simulation, Physics Simulation, and Resistor Color Code Calculator software for Windows.

Avogadro

Avogadro is a free molecular modeling software for Windows. It comes with a simple interface which offers a hassle-free chemical drawing. Some commonly used elements (carbon, oxygen, boron, fluorine, phosphorus, etc.) are available in its drop-down menu. Other elements can be selected from the built-in periodic table. Another drop-down menu is provided to select the order of bond as single, double, or triple. If you enable Adjust Hydrogens option, the software automatically adjusts the number of hydrogens in a molecular model. In addition to this, you can replace all the hydrogen atoms in a chemical structure with methyl.

You can perform the following actions on a molecular model:

• Change its label (name).
• Change the color of each atom of a molecular model.
• Change the radius of each atom separately in a molecular structure.

Moreover, you will also find a variety of display modes for a chemical structure: Van der Waals spheres, wireframe, simple wireframe, stick, etc. It also has an option to show or hide dipole moment, force, hydrogen bond, etc. in a molecular model.

Avogadro provides two types of views (perspective view and orthographic view) for every molecular model. You can directly insert the 3D structures of chemical groups, like alcohols, aldehydes, alkanes, alkenes, alkynes, amides, amino acids, carbohydrates, carboxylic acids, ethers, fatty acids, ligands, steroids, thiols, sulfoxides, etc. Moreover, you can also insert DNA and RNA structures. Before inserting a DNA or RNA structure, you can arrange the sequence of their bases. You can also select whether to insert a single-stranded DNA or double-stranded DNA.

Animation is an additional feature of this free chemistry drawing software.

After completing your project, you can save it in many different formats, like CML, XYZ, ENT, PDB, ALC, CHM, CDX, CDXML, C3D1, C3D2, SDF, SD, CHT, DMOL, GAM, INP, GAMIN, GAMOUT, etc. Apart from this, PDF, SVG, BMP, JPG, PNG, and POV-Ray are some of the formats to export a molecular model project.

Avogadro is a great molecular modeling software which comes with a lot of features. It is one of the best free molecular modeling software.

Ascalaph Designer

Ascalaph Designer is one more good molecular drawing software in this list. You can create molecular models of different compounds by selecting atoms from the periodic table. In order to launch the periodic table, you have to open the Free Drawing panel in the Build > Free drawing menu. Or, you can directly click on “Draw Molecule With Mouse” button available on its toolbar. In order to place the selected atom in the workspace, you have to press and hold Ctrl + Shift key. The Drawing panel comes with some more options along with the periodic table:

• You can add or remove hydrogen atoms with a single click.
• You can place a lone pair atom on the workspace.
• You can change the order of bonds as single, double, triple, aromatic, quadruple, quintuple, sextuple, septuple, and octuple.
• Kernel box: This box contains some commonly used structures which you can directly use in your chemical model. These structures include methane, ethene, water, ammonia, etc.

The Drawing Panel also shows the information of each atom in the periodic table by clicking on it. This information includes molecular mass of an atom, its electronic configuration, and length of covalent and Van der Waals bonds.

After drawing a molecular structure, you can analyze its temperature, pressure, dipole moment, quadrupole moment, energy, intermolecular energy, gradient, etc. Plus, it also has a geometry optimization feature, by which you can change the distance between two atoms, angle between two atoms, etc.

Talking about views, you can represent your molecular model in 5 styles: ball and stick, wireframe, wireframe CPK, CPK, and stick.

It lets you save the molecular model in mim, hin, mmol, smol, xmol, etc.

All in all, Ascalaph Designer is a great software to design molecular structures. Download it now.

ArgusLab

Download ArgusLab, a free chemistry drawing software and create different chemical models. Using this free chemistry software, you can draw the chemical structures of various compounds easily. You can select any element to make a chemical structure from the built-in periodic table. All the atoms that you placed on your model are available on the left side of the software for easy access.

In the Edit menu of the software, you will find an option named Auto Bonds. Enabling this feature will form chemical bonds among the atoms of a compound. By default, it forms the single bond between two atoms. You can change single bond to double, triple, or hybrid bonds easily by right clicking on that bond. Moreover, various rendering options are available to represent a chemical structure. You can set render mode to Wireframe, Cylinder Low, Cylinder Medium, BallCylinder Low, BallCylinder Medium, BallCylinder High, etc.

Talking about hydrogen atoms, you can add all hydrogen atoms to the chemical structure with a single click. However, you can also add them one by one manually. Besides this, you can also change the color of an atom.

ArgusLab also allows you to perform Gaussian Calculations, Energy Calculations, Optimize the Geometry of a chemical model, Electronic Spectrum Calculations, Dock Base Calculations, etc. Each of the available calculations can be customized by setting values of different parameters. For example, I can optimize the Geometry Calculation by changing different parameters such as Gradient Conversion, Maximum Iterations, RHF, etc.

Basic features like zoom in, zoom out, rotate, move, etc. are also available.

For convenience, some basic structures of rings and amino acids are provided in the software. You can use these structures directly in your molecular model. Following are some of the available structures:

• Rings: Cyclopropane, Cyclobutane, Cyclopentane, Cyclohexane-Chair, Cyclohexane-Boat, Anthracene, Pyrimidine, Pyrrole, indole, etc.
• Amino Acids: L-alanine, L-arginine, Glycine, L-serine, L-tryptophan, L-isoleucine, L-histidine,L-proline, etc.

After creating a chemical model, you can save it to different formats: AGL, PDB, MOL, etc. In addition to this, you can also export the chemical model in different graphics formats (BMP, JPG, POV, and TIFF).

MoluCAD

MoluCAD is another free chemical drawing software to draw chemical models. It lets you draw chemical structures in both 2D and 3D modes. Some commonly used elements to make a chemical structure are available on the right panel of the software. Other elements can be added to the chemical model from periodic table. You can launch the periodic table from the View menu.

Four different views are available for each chemical structure, namely, top view, front view, side view, and oblique view. You can connect all atoms in a molecule with single, double, triple, or hybrid bonds. Besides this, you can also change any atom or bond of a molecule by right-clicking on it.

Render Modes: You will get more than 5 render modes to represent a chemical structure. These include Ball & Stick 1, Ball & Stick 2, Ball & Stick 3, Space Fill, Pipes, Constellation, etc.

MoluCAD comes with a large number of pre-designed molecular structures categorized in different folders:

• Cool Files: The molecules which you will find here include Apoprotein, Aspartame, Binding Proteins, Biotin-Binding Proteins, Coagulation Factor, Complex Binding Protein, Crystalline, Conotoxin, Cytokine, DNA, DNA Binding Regulatory Protein, Kinase, Lyase, Photoreceptor, Plant Seed Protein, RNA, Ribosomal Protein, Toxin, Zinc Metalloprotease, and a lot more.
• Elements: Some common elements like Carbon, Bromine, Boron, Oxygen, etc. are available here.
• Functional Groups: Alkyl Groups, Acetyl, Alcohol, Alkene, Aldehyde, Carboxyl, Ether, Ester, etc. are some of the functional groups which you can access from here.
• Molecules: Amino Acids, Acetophenone, Acetyl Chloride, Azulene, Benzene, Benzoic Acid, Carbonyl Dicyanide, Ethyl Bromide, Naphthalene, etc. are provided in this section.

You can animate your created chemical models. The animation will spin the molecular structures at a speed set by the user. While the animation is running, you can vary the speed of each axis of the molecular model separately.

Query is an important feature of MoluCAD. It lets you calculate the distance between two atoms, bond length, bending angle, torsion angle, total mass of the cluster, etc.

It saves the project in its own supported MCD file format. But, you can export the project in different formats, like JPEG, Windows Bitmap, MDL Molfile, ASCII Text File, etc.

YASARA

YASARA is yet another molecular modeling software for Windows. It is a great software to create and simulate single molecular structures, like Methane (CH4), Borane (BH3), etc. But, I was unable to create the chemical structures that contain more than one molecule such as Ethane (C2H6), Butane (C4H10), etc. It also has an option to add all the hydrogens to an atom/molecule in a single click. If I talk about the basic features, you can do the following with a chemical model:

• Add/Delete hydrogens.
• Split molecule/residue/atom.
• Join molecule/residue/atom.
• Color molecule/residue/atom.
• Change the style of molecule/residue/atom as Ball, Ball & Stick, and Stick.
• Zoom in or out the model, etc.

It also lets you change the geometry of a chemical model by inflating or deflating the atoms. The properties of atom and the scene content are available on the screen. Moreover, it also has an auto-rotate button, clicking on which the molecular models starts rotating.

You can save your created molecular model as YASARA Scene, YASARA Object, PDB File, Normal Screenshot, etc.

Jmol

Jmol is an open source molecular modeling software based on JAVA. It does not have many advanced features as compared to other molecular modeling software in this list, but still, it is a good molecular modeling software. You can easily create chemical structures of different compounds. Moreover, adding or changing bonds in a chemical compound is not a difficult task.

Some commonly used elements (carbon, oxygen, hydrogen, nitrogen, fluorine, chlorine, etc.) are available in the list to make chemical structures. If your chemical model requires elements other than the available ones, you need to add them manually by writing their symbol, say Zn for Zinc. You can add a maximum of 9 elements for each chemical compound.

The unavailability of the periodic table in the software makes it quite unstable for molecular modeling.

Multiple views are provided for a model: top, left, right, bottom, and front. Besides this, viewing at different axes option is also available.

You can also vary the Van der Waals forces among atoms to 15%, 20%, 25%, etc. Talking about bonds, you can display bonds in single wireframe structure or adjust their width as 0.10 Angstroms, 0.15 Angstroms, 0.20 Angstroms, etc. The entire molecular structure can be displayed in different styles, such as CPK Spacefill, Ball and Stick, Wireframe, etc.

The measurement tool lets you measure the distance between two atoms in a molecule. The measured distance is displayed in nanometer, Angstroms, and picometers. You can increase or decrease the bond distance by dragging an atom. It also has an option to animate the molecular structures.

After creating a molecular model, you can save it in JPG and POVRay formats. Moreover, you can also export it to a web page.