MOPLOT

Introduction

In our research (molecular, electronic structure, and rearrangements of radical ions) there is a need for rapid inspection of the nodal properties and the general shape of MO's from different quantum chemical calculations (e.g. selection of the active space for a MCSCF calculation).

The graphic tools implemented in GaussView, Spartan, CaChe, Hyperchem etc. visualize MO's as three-dimensional electron density plots which take some time to calculate and do not always readily yield insight into the nodal structure of MO's.



HOMO of admantylidene displayed by GaussView (left) and MOPLOT (right)

MOPLOT fills this gap by producing 2-D projected images of geometries, MO's and normal vibrations produced immediately from the output of various standard quantum chemical programs.

Hardware requirements

Unlike the previous version of MOplot which was written in Microsoft Fortran and was therefore tied to Microsoft operating systems (and hence to Intel-based hardware), the new version has been completely rewritten from scratch by Dr. Rouslan Olkhov using the LabView programming environment which is available for Windows, the Mac OS, Linux, and Solaris.

Thanks to this, MOplot runs now on the vast majority of currently available PCs and workstations. We have tested it on different PCs under Windows 98, Windows XP, under Red Hat Linux 6, and under Mac OS X (users who wish to get a version of MOPlot for Mac OS 9 should contact the authors). Of course MOplot can also be launched under Linux inside an X-Window terminal on any PC which has a program to emulate such a terminal (e.g. Exceed, Exodus)

MOplot comes compiled into an executable, so users do not need LabView to run the program. However, the executable makes runtime calls to libraries that must be present on the same Computer. Installers for these runtime libraries are provided for Windows, Linux, and Mac OS X. Installation of the runtime libraries must only be effected once, later updated executables can be downloaded from this website and run without further ado, provided that they make calls to the same version of the LabView Runtime engine (if there is an incompatibility, e.g. because you have already a version of LabView installed on our computer, it will tell you, then the LabView Runtime engine that is delivered with MOPplot must be installed over the existing one).

Since the MOplot performs a lot of mathematical operations, response of the program may be sluggish on obsolete hardware. In our experience, a 1 GHz Intel or Athlon or a 600 MHz G3 PowerPC processor based system with at least 64 MB of free memory is the minimum that is needed to get acceptable performance. A fast good graphics card helps, too.

Moplot reads directly the output of quantum chemical programs (see below). Unless MOplot runs on the same workstation where the quantum chemical calculations are carried out, it is very practical to have direct network access to the workstation disk where these outputs are stored, such as to avoid cumbersome file transfers.

Features of MOplot

• MOplot can display:

• geometries, including the cartesian coordinate axes, atom numbers according to the geometry definition in the calculation. Molecules can be turned in all directions under mouse control, or using the controls in the "camera" menu.

  In the "geom" menu, geometric parameters (bond lengths, angles, dihedrals) can be computed for any set of atoms or midpoint between atoms (the latter is a unique feature of MOplot)

  MOplot reads all the steps of a geometry optimization, so this process can be inspected visually ("extra" menu)

• Mulliken atomic charges, group charges (charges of hydrogens summed into heavy atoms), atomic spin populations (for open shell systems), of course only if the corresponding information is available in the output of the calculation.

• Molecular orbitals (hence the name of the program), according to the protcol defined by Haselbach and Schmelzer and described below. MO's can be RHF; UHF alpha/beta (cf switch in the "MO" menu). CASSCF, NO's). SCF MOs are ordered by energies, CASSCF MOs are ordered by occupation numbers.

  It is a unique feature of MOPlot that the user can rapidly toggle through MOs, which is not possible with any other program know to us (and the reason why we developed MOplot). Also the molecules can be turned around freeely with the MO's on.

• Normal vibrations, both as displacement vectors and in animated form. For complex molecules where the calculation of the displacements may become slow, a "loop" mode is available to speed up the animation.

Linear combination of vibrations can be formed. This feature is useful to visualize the movement of atoms along degenerate normal modes (presently the different frequencies of nondegenerate modes are not taken into account).

• MOplot can generate (interpreted or encapsulated) postscript output in vector format. Pages can be freely configured to hold multiple images of any kind that can be displayed on the screen. MOplot output can be imported into most current drawing programs (AI, CorelDraw …) for further processing

MOplot is presently configured to recognize output from GAUSSIAN (G94, G98, and G03) and GAMESS calculations (not all options supported in the latter), as well as input to the Molden backend, such as it is for example generated by the Molcas program. In addition, we have defined a proprietary standard format which MOplot also recognises. Sample files written in that format can be downloaded below. Uses who want to interface MOplot to their favourite quantum chemical program should write scripts that convert the output of that program into the standard format.

• All colors and fonts that appear in the various displays can be freely configured by the user ("misc" menu). A toggle is available to switch between color and b/w renditions, e.g. for publication purposes.

Rules for drawing MO's (Haselbach and Schmelzer, 1971)*

An LCAO-representation of MO's is given in the ZDO approximation (no overlap densities). AO contributions are:

• displayed as single spheres (pure s-AO's), or pairs of contiguous spheres (pure p-AO's) whose (combined) area is proportional to the contribution of an AO to the electron populatio at the atom on which this AO is centered

• In s/p hybrid MO's, the area of one sphere is enlarged relative to the other in proportion to the size and sign of thes-contribution. If c(s)>c(p), a single sphere is drawn whose center is displaced in the direction of the (px,py,pz) vector in proportion to the p-contribution. (in MOplot, the s/p ratio threshold where the display switches from pairs of spheres to single spheres can be changed. The default value is 1)

Ab-initio MOs, inner and outer contributions from double- or triple-zeta basis sets are simply added up, and polarization functions are ignored. After that MOs are renormalized to 1.

* Helv. Chim. Acta 54, 1299 (1971)

Example: Methyl cation

Limitations, Caveats

It is important to remember that MOplot was originally developed for viewing the results of semiempirical calculations to which the ZDO approximation is inherent. Its MO display mode reflects these theoretical models and MOplot should therefore not be regarded as a program that yields accurate renditions of ab-initio wavefunctions. If this is required, users should resort to one of the many fancy electron density plotting packages (e.g. Spartan, Molekel) which do an admirable job at that. The main purpose of MOplot is to gain quick insight into the nodal properties of MOs and their approximate distribution over a molecule. These features can be more easily recognized in a ZDO-type rendition, such as it is provided by MOplot.



MOplot knows only about AO-coefficients, it ignores that fact that the same AOs have different exponents in different atoms. As long as one stays in the CHON group and within the realm of valence MOs, the errors introduced by this are usually tolerable, but if one does e.g. hydrogen fluoride, the results have very little relation to reality with regard to the electron distribution. Also, to keep things simple, the contributions of inner and outer split valence basis AO's are simply summed up and polarization functions are ignored. After this, MOs are renormalized to one, to make them comparable among each other.



MOplot is not a commercial piece of software, and we can assume no responsibility whatsoever with regard to its performance. We have tested it to the extent that we can, and it looks as though it runs quite reliably. Nevertheless users are very likely to encounter bugs here and there and we would be very indebted if users would take the time to communicate these bugs to us.

How to obtain MOplot

Depending on the platform you wish to use it on, click on one of the below links:


• MOPlot-version-1.82.tar.gz zipped tar file for Linux
  
• MOPlot-version-1.83.sitx stuffed file for Macintosh OS X (Macs with G3-G5 processors) *)
  
• MOPlot_OS-X_Intel.sitx stuffed file for Macintosh OS X (Macs with Intel processors) *)
  
• MOPlot-version-1.85.zip zipped file for Windows
  

Here you can find MOplot manual (pdf):

• Manual
  

and here the sample files for the propietary MOPLot input format:

• Sample files
  

The authors would be grateful to learn about your opinion on MOplot and possible bugs in the program.

They can be reached via:

• Thomas Bally (Thomas.Bally@unifr.ch)