PMI plot

Principal Moments of Inertia (PMI)

PMI plots are often used to visually represent the 3D shape diversity of compounds of a collection in “molecular shape space” spanned by the three basic extreme shape types: “rod-like” (e.g., acetylene), “disk-like” (e.g., benzene) and “spherical” (e.g., adamantine).[REF]

Method

Here Experimental Torsion Distance Geometry(with Knowledge) ETKDG, implemented in the open-source cheminformatics library RDKit, was used for the energy minimizations to generate 3D conformers for each compound. Normalized PMI ratios (I1/I3 and I2/I3) of these conformers and then plotted on a triangular graph, with the coordinates (0,1), (0.5,0.5) and (1,1) representing a perfect rod, disc and sphere, respectively [REF].

* THE CALCULATION MAY TAKE A FEW MINUTES.

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Examples

Here are some papers using PMI diagrams as a way to analyze the shape diversity of their compounds:

Kopp F, Stratton C F, Akella L B, et al. Diversity-oriented synthesis approach to macrocycles via oxidative ring expansion[J]. Nature chemical biology, 2012, 8(4): 358. link, data set download

Beckmann H S G, Nie F, Hagerman C E, et al. A strategy for the diversity-oriented synthesis of macrocyclic scaffolds using multidimensional coupling[J]. Nature Chemistry, 2013, 5(10): 861. link, data avialable here

Ibbeson B M, Laraia L, Alza E, et al. Diversity-oriented synthesis as a tool for identifying new modulators of mitosis[J]. Nature communications, 2014, 5: 3155. link

Gerry C J, Hua B K, Wawer M J, et al. Real-time biological annotation of synthetic compounds[J]. Journal of the American Chemical Society, 2016, 138(28): 8920-8927. link

Nie F , Kunciw D L , Wilcke D , et al. A Multidimensional Diversity‐Oriented Synthesis Strategy for Structurally Diverse and Complex Macrocycles[J]. Angew Chem Int Ed Engl, 2016, 55(37):11139-11143. link


Herrera L, Barrio P, Ibáñez I, et al. 8-Iodonaphthalene-1-carbaldehyde: a versatile building block for diversity-oriented synthesis[J]. Organic letters, 2016, 18(18): 4722-4725. link

Ciardiello, J. J., et al. "A novel complexity-to-diversity strategy for the diversity-oriented synthesis of structurally diverse and complex macrocycles from quinine." Bioorganic & medicinal chemistry 25.11 (2017): 2825-2843. link

Chawner S J , Cases-Thomas M J , Bull J A . Divergent Synthesis of Cyclopropane-Containing Lead-like Compounds, Fragments and Building Blocks via a Cobalt Catalyzed Cyclopropanation of Phenyl Vinyl Sulfide[J]. European Journal of Organic Chemistry, 2017. link

Alejandro GuarnieriIbáñez, Medina F , Céline Besnard, et al. Diversity-Oriented Synthesis of Heterocycles and Macrocycles by Controlled Reactions of Oxetanes with α-Iminocarbenes[J]. Chemical Science, 2017, 8(8):5713. link

Vu H, Pedro L, Mak T, et al. Fragment-Based Screening of a Natural Product Library against 62 Potential Malaria Drug Targets Employing Native Mass Spectrometry[J]. ACS infectious diseases, 2018, 4(4): 431-444. link (Fragment PMI Plot)

Santos, Marilia S., et al. "Synthesis of Highly Substituted 1, 2‐Diazetidin‐3‐ones, Small‐Ring Scaffolds for Drug Discovery." Chemistry–A European Journal (2018). link

Choi, Yoona, Heejun Kim, and Seung Bum Park. "A divergent synthetic pathway for pyrimidine-embedded medium-sized azacycles through an N-quaternizing strategy." Chemical Science (2019). link

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