Published online 2013 Dec 6. doi: 10.6026/97320630009988
PMID: 24391363
This article has been cited by other articles in PMC.
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Abstract
Building 3-dimensional (3D) molecules is the starting point in molecular modeling. Conformer search and identification of a globalenergy minimum structure are often performed computationally during spectral analysis of data from NMR, IR, and VCD orduring rational drug design through ligand-based, structure-based, and QSAR approaches. I herein report a convenient script thatallows for automated building of 3D structures and conformer searching from 2-dimensional (2D) drawing of chemical structures.With this Bash shell script, which runs on Mac OS X and the Linux platform, the tasks are consecutively and iteratively executedwithout a 3D molecule builder via the command line interface of the free (academic) software OpenBabel, Balloon, andMOPAC2012. A large number of 2D chemical drawing files can be processed simultaneously, and the script functions withstereoisomers. Semi-empirical quantum chemical calculation ensures reliable ranking of the generated conformers on the basis ofenergy. Mac apps cleanmymac x 4.2.1. In addition to an energy-sorted list of file names of the conformers, their Gaussian input files are provided for ab initio anddensity functional theory calculations to predict rigorous electronic energies, structures, and properties. This script is freelyavailable to all scientists.
Keywords: 3D structure generation, conformer search, shell script, free software
Background
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Building 3-dimensional (3D) structures of molecules is astarting point for computational analysis because physical,chemical, and biological properties of a molecule are related toits 3D structure. Observed physicochemical properties reflectthe statistical average of all possible conformations, and arepredominantly associated with the global energy minimumstructure and its periphery. Thus, conformational space forflexible molecules is often explored after 3D structuregeneration to find minimum energy structures, i.e., conformers.Searching for conformers, finding the global energy minimumconformer and its periphery, and taking into account theBoltzmann distribution can help with the spectral assignmentduring spectroscopic analysis such as NMR, IR, and VCD. Forrational drug design, searching for conformers is a crucial stepbecause most drugs have an optimal bioactive conformation inthe active site of their target biomolecule, and this conformationis likely to be close to that of low-energy conformers.
I herein report a free script for automated building of 3Dstructures and conformer searching based on 2-dimensional(2D) drawing of chemical structures. This is a Bash shell script,and runs on Mac OS X and the Linux platform. Without a 3Dmolecule builder, the tasks are consecutively and iterativelyexecuted via the command line interface and free (academic)programs OpenBabel [1,], Balloon [3,], and MOPAC2012 [5,]. There are many commercial applications for conformergeneration using a 3D molecule builder []. On the other hand,scientists are familiar with 2D skeletal formulas, and benchscientists routinely draw 2D chemical structures using moleculeeditor such as ChemDraw [8] or MarvinSketch [9]. Theproposed script is convenient in this regard, and processes alarge number of 2D chemical drawing files simultaneously. Italso functions with stereoisomers. Energy-minimizedconformers are generated using a force field, and are furtherprocessed using semi-empirical quantum chemical calculationsto estimate their heats of formation. In addition, input files forab initio and density functional theory (DFT) calculations aredumped to predict rigorous electronic energies, structures andproperties. After completion of all energy calculations of thegenerated conformers, an energy-sorted list of file names of theconformers is provided.
Settings
OpenBabel is a freely available chemistry toolbox designed toaccept inputs in all languages that are used for processingchemical data, and was installed in /usr/local/bin. Theexecutable babel (version 2.3.1 for Mac and 2.3.2 for Linux) isused to convert file formats and to generate input files forMOAPC2012 and Gaussian09 [10] in the script.
Balloon is a freely available tool that generates 3D atomiccoordinates from molecular connectivity via distance geometry,and conformer ensembles by using a multi-objective geneticalgorithm (GA). This tool also considers stereochemistry ofdouble bonds and tetrahedral chiral atoms. The executableballoon (version 1.4.1.1068 for Mac and Linux) was installed inthe home directory, and is used for addition of hydrogen atomsto a skeletal formula, generation of a 3D model and itsconformers, and energy minimization using a MMFF94-likeforce field.
MOPAC2012, a free academic program, is a general-purposesemi-empirical molecular orbital package for studying solidstate and molecular structures and reactions. The executableMOPAC2012.exe (version 13.306 for Mac and Linux) wasinstalled in /opt/mopac and is used for single point energycalculation by the PM7 method.
Input & Output
When the shell script confs.sh (see supplementary material) isrun in a working directory, it reads the file name of a 2Dchemical structure saved in MDL SDfile (.sdf) format (i.e., the atomsare recorded as coordinates), and creates a new directory with thefile name. In the new directory, hydrogen atoms are added tothe skeletal formula, and 100 3D conformers, minimized withthe MMFF94-like force field, are generated as a single outputmolecule entry in the .mol2 file format. After each conformerput into consecutively numbered files, its single point energycalculation is performed using the PM7 method inMOPAC2012. After completion of the calculation, the heat offormation is printed in kcal/mol in a text (.txt) file. The scriptalso dumps a short summary (.arc) file of computational resultsincluding the geometry, and its converted (_1scf.sdf) file. These(.mol2, .arc, and _1scf.sdf) files are accessible for visualverification of the geometry using a molecular viewer such asJmol [11,], ViewDock in Chimera [13,], and DS Visualizer[15]. The Gaussian input (.com) file is also generated forgeometry optimization and vibrational analysis through highlevelquantum chemical calculation. After completion of allsingle point energy calculations, an energy-sorted list of filenames of the conformers is dumped with the extension .xls inthe same directory. The lowest-energy conformer can beconsidered as the global energy minimum structure. As shownin (Figure 1 & Figure 2), the lowest-energy conformers being close tothe X-ray crystal structures of the small molecules [,] werepredicted as a result of selecting adequate options andkeywords for Balloon and MOPAC2012. These data would beconfirmed through high-level ab initio and DFT calculation forthe several low-energy conformers. The Boltzmann distributionof optimized conformers at certain temperature can beestimated from their energies [].
(Top) skeletal formula of 1,4-bis(hexyloxy)benzene;(bottom) superposition of the X-ray crystal structure (graycarbon) [] with the lowest-energy conformer (cyan carbon).The superposition was done using DS Visualizer. https://avatree804.weebly.com/blog/mac-photo-management-software-2017.
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(Top) skeletal formula of (3R,4S,5R)-methyl 3,5-bis[(tert-butyldimethylsilyl)oxy]-4-methoxycyclohex-1enecarboxylate; (bottom) superposition of the X-ray crystalstructure (gray carbon) [] with the lowest-energy conformer(cyan carbon). The superposition was done using DS Visualizer.
As mentioned above, this script runs on Mac OS X and theLinux platform, and can process a large number of chemicaldrawing files simultaneously.
Caveat & Conclusion
When working with any stereoisomer, a user must check thespatial arrangement of its atoms visually with one initial 3Dmodel (_3d.sdf) generated by an auxiliary shell scriptcheck3d.sh (see supplementary material). Suitablearrangements of atoms and choices of bonds in a 2D chemicalstructure will result in a desired 3D model. https://avatree804.weebly.com/blog/download-hp-utility-software-mac. The user shouldalways check the initial 3D model using check3d.sh beforerunning confs.sh. Open source MOPAC7 [19,20] can be used inplace of MOPAC2012, but the PM7 method cannot be processedin MOPAC7. The installation path names and Gaussiankeywords in the script should be changed accordingly.
In conclusion, this script integrates excellent free scientificapplications and has the following advantages: (i) 2D chemicaldrawing files are available as input; (ii) 3D molecules are builtand conformers are sampled without a 3D molecule builder;(iii) time is saved because of batch processing via the commandline, and (iv) accurate energies are provided along with inputfiles for high-level quantum chemical calculations. I hope thatthis free script will be useful for scientists who study moleculesusing experimental and computational methods.
Supplementary material
Data 1:
Footnotes
Citation:Ishikawa, Bioinformation 9(19): 988-992 (2013)
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