MoCalc2012 Tutorial

MoCalc2012

System Requirements:

• 32-bit version: Min. 32 or 64-bit Windows XP SP3 and .NET-Framework 3.5
• 64-bit version: Min. 64-bit Windows 7 and .NET-Framework 4.6

Highlights of the program:

• Supports Linux versions of MO programs via Windows 10 Subsystem for Linux (WSL)
• Use 'JSME' or 'CH5M3D' as molecule editor or your favorite external editor (e.g.'Avogadro' or ACD's 'ChemSketch').
• Smooth integration of 'ChemSketch' via Chembasic-scripts.
• Fully editable Z matrix builder/editor.
• Import existing XYZ, MOL, PDB, CML, SMILES/Inchi and crystallographic structures directly into the program
• Import existing G9x, Gamess, TINKER, NWChem, ORCA, Mopac and input/output files from other MO programs directly into the program.
• 'Drag and Drop' (for files and text) and 'Copy and Paste' (for text) functionality. Integration with system clipboard.
• Download structures from PubChem, NCI/CADD Chemical Identifier Resolver and Protein Data Base
• Extensive filtering options for files containing multiple structures.
• Detection of molecular point groups and symmetrization of nearly symmetric molecules.
• Molecular Mechanics based optimization and conformer search prior to MO calculation.
• Enter keywords via template, editor or read from files.
• Restricted/relaxed 1D and 2D reaction path/grid calculations.
• Constrained optimizations.
• Modeling of proteins (MOPAC).
• Display of results using browser-based JSmol-application (geometry, orbitals, surfaces, animations, vibrations)
• Java based Jmol(included) or wxMacMolPlt(for GAMESS/Firefly) may be used as alternate viewers.
• Summaries for GAMESS/Firefly/NWChem/ORCA calculations.
• Export of optimized structures to a multitude of file formats.
• Run MO programs as internal tasks or kick off as external processes.
• Batch processing.
• Job Manager for Job Organization and Control.
• Creation of spreadsheet summaries to compare results from multiple jobs.

Display of Electronic Surfaces:

Electron Density
Spin Density
Electrostatic Potential
Fukui's FMO Susceptibilities
Electron Localization Function (ELF)
Non Covalent Interactions (NCI)
Mulliken-, Loewdin- and AIM-Charges; Dipolemoment

Display of diagrams:

Energy Level Diagrams
Total(TDOS), Partial(PDOS) and Overlap Population(OPDOS) Density-Of-State Plots
SCF/Geometry Convergence Diagrams
Interactive window showing the correlation of the energy to the structures along the reaction coordinate
Interactive window showing the decline in energy versus the structures along the optimization path
Interactive correlation of animated vibrations to IR/Raman bands

Display of spectra:

(Anharmonic)IR,Raman spectra
UV/VIS/CD spectra
1H- and 13C-NMR spectra
XAS/XES spectra
NRVS spectra

• Scaling of vibrational frequencies and conversion of NMR tensors to chemical shifts via basis-set dependent parameters.
• Comparison of calculated and experimental spectra (JCAMP-DX or graphics formats).
• Detailed analysis of UV/VIS spectra.
• Download of experimental spectra from ChemSpider, NIST Chemical WebBook, NMRSHIFTDB or SDBS Spectral Database
• Export of all diagrams and spectra to spreadsheet format
• Export of picture files from trajectory animations for movie creation.
• Unit converter (energy,length, dipole moment).

• Lookup of properties for structures at public databases.

• Tool for NMR spectra simulation (up to 10 spin systems)

Acknowledgments:

• In the background this program makes use of OpenBabel: http://openbabel.org/; (see: Noel M O'Boyle, Michael Banck, Craig A James, Chris Morley, Tim Vandermeersch and Geoffrey R Hutchison, J. Cheminf. 2011, 3:33) and of the OBDotNet-API.

• JSmol: an open-source HTML5 viewer for chemical structures in 3D. http://wiki.jmol.org/index.php/JSmol#JSmol and

• Jmol : an open-source Java viewer for chemical structures in 3D: http://www.jmol.org/
  are both used to visualize structures, surfaces, vibrations and animations.
• JSME is used as 2D molecule editor: http://peter-ertl.com/jsme/. See also: B. Bienfait and P. Ertl, JSME: a free molecule editor in JavaScript, J. Cheminformatics 5:24 (2013)
• CH5M3D is used as 3D molecule editor: http://ch5m3d.sourceforge.net/index.html. See also: Clarke W Early, CH5M3D: an HTML5 program for creating 3D molecular structures, (http://www.jcheminf.com/content/5/1/46 ).
• The symmetrizing and electronic surface routines as well as the routines for putting the molecule to its standard orientation and The MOPAC Solvent-parameters were taken from 'Gabedit': http://sourceforge.net/projects/gabedit/, s. also: "A.R. ALLOUCHE, Gabedit - A graphical user interface for computational chemistry softwares, Journal of Computational Chemistry, 32, 174-182(2011)".

The following databases are contacted:

• Chemical Identifier Resolver: http://cactus.nci.nih.gov/chemical/structure
• PubChem: https://pubchem.ncbi.nlm.nih.gov/
• Protein Data Base: https://www.rcsb.org
• Protein Data Base Download: https://files.rcsb.org
• ChemSpider: http://www.chemspider.com/
• NIST Chemistry WebBook: http://webbook.nist.gov/chemistry/
• NMRSHIFTDB: http://www.nmrshiftdb.org/
• SDBS Spectral Database: http://sdbs.db.aist.go.jp
• Sigma-Aldrich: http://www.sigmaaldrich.com/catalog/search