Literature DB >> 28776208

The octet rule in chemical space: generating virtual molecules.

Rafel Israels1, Astrid Maaß1, Jan Hamaekers2.   

Abstract

We present a generator of virtual molecules that selects valid chemistry on the basis of the octet rule. Also, we introduce a mesomer group key that allows a fast detection of duplicates in the generated structures. Compared to existing approaches, our model is simpler and faster, generates new chemistry and avoids invalid chemistry. Its versatility is illustrated by the correct generation of molecules containing third-row elements and a surprisingly adept handling of complex boron chemistry. Without any empirical parameters, our model is designed to be valid also in unexplored regions of chemical space. One first unexpected finding is the high prevalence of dipolar structures among generated molecules.

Entities:  

Keywords:  Chemical space; GDB; Virtual chemistry; Virtual compounds; Virtual libraries

Mesh:

Year:  2017        PMID: 28776208     DOI: 10.1007/s11030-017-9775-2

Source DB:  PubMed          Journal:  Mol Divers        ISSN: 1381-1991            Impact factor:   2.943


  24 in total

1.  SCUBIDOO: A Large yet Screenable and Easily Searchable Database of Computationally Created Chemical Compounds Optimized toward High Likelihood of Synthetic Tractability.

Authors:  F Chevillard; P Kolb
Journal:  J Chem Inf Model       Date:  2015-09-04       Impact factor: 4.956

2.  Virtual exploration of the small-molecule chemical universe below 160 Daltons.

Authors:  Tobias Fink; Heinz Bruggesser; Jean-Louis Reymond
Journal:  Angew Chem Int Ed Engl       Date:  2005-02-25       Impact factor: 15.336

3.  Learning to predict chemical reactions.

Authors:  Matthew A Kayala; Chloé-Agathe Azencott; Jonathan H Chen; Pierre Baldi
Journal:  J Chem Inf Model       Date:  2011-09-02       Impact factor: 4.956

4.  ReactionPredictor: prediction of complex chemical reactions at the mechanistic level using machine learning.

Authors:  Matthew A Kayala; Pierre Baldi
Journal:  J Chem Inf Model       Date:  2012-10-01       Impact factor: 4.956

5.  The high-throughput highway to computational materials design.

Authors:  Stefano Curtarolo; Gus L W Hart; Marco Buongiorno Nardelli; Natalio Mingo; Stefano Sanvito; Ohad Levy
Journal:  Nat Mater       Date:  2013-03       Impact factor: 43.841

6.  Data mining with molecular design rules identifies new class of dyes for dye-sensitised solar cells.

Authors:  Jacqueline M Cole; Kian Sing Low; Hiroaki Ozoe; Panagiota Stathi; Chitoshi Kitamura; Hiroyuki Kurata; Petra Rudolf; Takeshi Kawase
Journal:  Phys Chem Chem Phys       Date:  2014-12-28       Impact factor: 3.676

7.  Stochastic voyages into uncharted chemical space produce a representative library of all possible drug-like compounds.

Authors:  Aaron M Virshup; Julia Contreras-García; Peter Wipf; Weitao Yang; David N Beratan
Journal:  J Am Chem Soc       Date:  2013-05-02       Impact factor: 15.419

Review 8.  Heterocyclic N-Oxides - An Emerging Class of Therapeutic Agents.

Authors:  A M Mfuh; O V Larionov
Journal:  Curr Med Chem       Date:  2015       Impact factor: 4.530

9.  Understanding and classifying metabolite space and metabolite-likeness.

Authors:  Julio E Peironcely; Theo Reijmers; Leon Coulier; Andreas Bender; Thomas Hankemeier
Journal:  PLoS One       Date:  2011-12-14       Impact factor: 3.240

10.  The Chemistry Development Kit (CDK): an open-source Java library for Chemo- and Bioinformatics.

Authors:  Christoph Steinbeck; Yongquan Han; Stefan Kuhn; Oliver Horlacher; Edgar Luttmann; Egon Willighagen
Journal:  J Chem Inf Comput Sci       Date:  2003 Mar-Apr
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