Classification of Organic Molecules by Molecular Quantum Numbers

Abstract

The periodic table classifies elements by increasing atomic number in periods following the principal quantum number, and allows their physicochemical properties to be rationalized.[1] Herein, we propose a related system for organic molecules based on 42 molecular quantum numbers (MQNs), defined here as counts for simple structural features such as atom, bond and ring types, creating a multidimensional grid called MQN space. In analogy to the elements and their isotopes grouped in each entry of the periodic table, MQN isomers have identical MQNs and occupy the same position in MQN space. The MQN system is able to analyze large molecular databases and clusters compounds with similar structure, physicochemical properties and bioactivities, as illustrated for the databases ZINC [2] and GDB-11.

Visualisation of the chemical space of fragments, lead-like and drug-like molecules in PubChem

“…[11]) written in Java using the JChem library from Chemaxon, Ltd. Prior to MQN-calculation, the ionization state of each structure was adjusted to pH 7.4 using the JChem API.…”

Visualisation and subsets of the chemical universe database GDB-13 for virtual screening

“…The most occupied MQN-bin contained 12,589 molecules, while 4,959,920 MQN-bins contained only one molecule (Fig. 1) [19]. Principal component analysis (PCA) was performed to gain an insight into the data structure.…”

“…[19]) written in Java using the JChem library from Chemaxon, Ltd. Prior to MQN-calculation, the ionization state of each structure was adjusted to pH 7.4 using the JChem API.…”

“…At present however such exploration is limited by the currently available virtual screening methods, which typically process at most a few million structures within resonable computing time. To address this limitation, we recently reported a molecule classification method for large databases called the MQNsystem [19]. This system places organic molecules in a chemical space [18,[20][21][22] on the basis of 42 integer value descriptors for structural and topological features, called MQNs (Table 1).…”

Exploring Chemical Space for Drug Discovery Using the Chemical Universe Database

“…23 We recently proposed a set of 42 integer value descriptors called molecular quantum numbers (MQNs). 25 MQNs count elementary features of molecules including atom and bond types, polar groups, and topological features, which are all easily identified in a structural formula by anyone with basic knowledge of organic chemistry ( Table 2). The MQN system defines a simple and universal chemical space to classify organic molecules, in analogy to the periodic system classifying the elements according to their atomic and principal quantum numbers.…”