Marion Nanosystems - Molecular Builder

Molecular Builder

Build complex molecules with a few mouse clicks. Take predefined

samples from the Molecule Cupboard as building blocks; edit,

combine and extend them to new molecules. Change chemical

elements, hybridization type, angles, and bond lengths.

How do you think about molecules? As a bunch of individual atoms, each with its own set of spatial coordinates? As composed of smaller subgroups, such as benzene rings with attached functional groups? If you prefer the latter, you will enjoy Atomistix Molecular Builder.

§ Combine smaller atomic subgroups to complex molecules.

§ Select predefined molecules from the Molecule Cupboard.

- aromatic rings, amino acids, functional groups, …

§ Add atoms directly in the 3D view. Hydrogen atoms are automatically inserted.

§ Extend, edit, and fine-tune existing molecules.

Atomic coordinates are abandoned

With the new Molecular Builder one of the major obstacles encountered in traditional, so-called academic*, electronic-structure codes is overcome, namely the cumbersome and error-prone way to set up molecular geometries. In these codes, typically, you are asked to calculate and to key in spatial coordinates of individual atoms. Even for a fairly small molecule with, say, 20 atoms, this is an overwhelming task with 60 atomic coordinates to be calculated.

The main problem, however, is not that it is time-consuming and rather boring, but that mistakes are almost unavoidable. Accidentally interchanging some numbers can result in a molecule with completely different properties than intended!

In addition, the whole atomic-coordinate approach itself is unappealing and non-intuitive especially to scientists and engineers who tend to think about molecules in terms of benzene rings, functional groups, and other building blocks.

The Molecular Builder takes, in contrast to traditional codes, advantage of the building block idea and contains a Molecule Cupboard with a broad selection of predefined molecules, from simple diatomic ones to amino acids. Use them directly, or as building blocks.

With its minimalistic design the Molecular Builder differs from other molecule constructors available on the market. The clean and compact interface is not overloaded with menus and icons. All functions are available directly; there is no need to switch to a “distance mode” to change bond lengths or an “angle mode” to change angles.

Pattern recognition speeds up your work

In the 3D View, you can add atoms directly using either your keyboard or the Periodic Table. Pattern recognition determines the optimized geometry by searching through an extensive database of molecular templates.

As a concrete example, consider water. The easiest way to build a water molecule is to insert a single oxygen atom by pressing the 'O' key on the keyboard. Since oxygen by default is sp3-hybridized and known to hold two lone pairs, two hydrogen atoms are automatically inserted and bonded to the oxygen atom in a planar geometry. The molecular geometry is automatically adjusted such that the bending angle (the H–O–H angle) and the bond lengths are set to experimentally determined equilibrium values. This means that the bending angle is set to 104° and not 109.5° as in an idealized tetrahedral geometry.

To construct a biphenyl molecule (lemonene), select two benzene rings from the Molecule Cupboard and replace one of the hydrogen atoms with a carbon atom of another benzene ring. Using pattern recognition, the Molecular Builder adjusts the geometry such that the two rings are tilted 45° with respect to each other.

The automated process makes molecular modeling fast and easy. Still, you are in total control. Edit and fine-tune your molecules in the Geometry Manager. Change:

§ chemical elements

§ hybridization type

§ bond order

§ bond lengths and bond angles

§ dihedral angles

Let us consider ethane. To turn the default

staggered conformation to eclipsed ethane

just change the dihedral angle.

With the Molecular Builder, you focus on the

chemical properties of your molecules.

The Molecular Builder is primarily intended for modeling smaller organic molecules, e. g. in molecular electronics. Though formally there is no upper limit to the molecule size, designing proteins containing several thousands of atoms is in practice prohibited by the resolution. Working with a couple of hundred atoms or so is however not a problem.

* "academic" indicates that the codes are developed and maintained by academic researchers.

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