Molecules Explorer

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Welcome to the Molecules Explorer wiki!

You will find in here all relevant information regarding the Molecules Explorer App, including release notes, the manual, etc.

Release Notes

Recent changes

Version 0.1 - July 16, 2016

  • Initial release of Molecules Explorer.

Introduction

The primary goal of the molecular explorer is to report the atomic structure of molecules, found using quantum chemistry computational methods. Further quantities of interest, including the electron affinity (EA) and ionization energies (IE), are also reported.

Manual

Calculations

The methodology used to compute the atomic structure is a standard quantum chemical approach. This involves solving Schrodinger’s equation using both a linear combination of atomic orbitals (LCAO) with a relevant functional to address the question of the potential. The LCAO were implemented with the use of the 6-31+* Pople basis [1] and the hybrid-functional B3LYP was used [2].

Using the Computational Molecular Explorer

In order to search the database for the molecule in question, four methods can be employed.
1) Elements : returns any entry that includes the queried elements
2) Formula : returns any entry that satisfies a permutation of the queried atoms (e.g. H2O1, H2O, HOH, OHH all return water)
3) InChi (The IUPAC International Chemical Identifier): uses “bond connectivity, tautomeric information, isotope information, stereochemistry, and electronic charge information.” (See InChI Wikipedia) This may be the most precise way of searching for a molecule but perhaps the most complicated.
4) Chem Doodle: allows drawing of the chemical structure to query for the database entry (currently not supported on Firefox)

References

  1. Ditchfield, R., Hehre, W.J. & Pople, J.A. J. Chem. Phys. 54, 724 (1971)
  2. Becke, A.D. Phys. Rev. A. 38, 3098 (1988)