Software

Visualization of Molecular Orbitals in WebMO

WebMO program can be used for visualization of molecular orbitals (MOs) from Q-Chem or other packages interfaced with it (e.g. GAMESS). To visualize the MO select a job in „Job Manager“ by clicking on „View Job“ (icon with magnifying glass) then scroll down the window and select an orbital from the Molecular Orbitals list. The orbital will be plotted in the „MO Viewer“ window.

Unfortunately, WebMO version 9.1.002e has a bug which gives the error message: „Attempting to set MO coefficient >= MAX_AOS“ if you try to visualize relatively large molecule (larger than benzene). This problem can be fixed using a short Perl script. Use the following instructions to plot MOs of larger molecules:

1. On „View Job“ page from the list of Molecular Orbitals by clicking on the icon with a diskette download any one orbital. The file will have .mo extension and contain information about ALL orbitals in your molecule. For example, this file can be named as mymol.mo.

2. Then using a Perl script mofilter.pl (see the download link below) and mymol.mo file as an input parameter generate a series of .mo files (e.g. mymol_001.mo, mymol_002.mo etc.). Each file now contains information about one MO of your molecule and a number in its name shows the orbital's number. Use the following command to generate these files:
perl mofilter.pl mymol.mo

Download: mofilter.zip (1.9KB)

3. On „View Job“ page of WebMO select „MO Viewer“ tab and using File/Open menu open generated .mo files (e.g. mymol_001.mo) to visualize them.

Notes:
a. To verify orbital numbers always check MO energies either on „MO Viewer“ panel or inside .mo file. In .mo file orbital energy is printed on the line next to the line which contains text: „[MO“.
b. To run mofilter.pl script a Perl interpreter should be installed on your computer. If you use Windows then you can use active Perl.

Q-Chem Development

For offcial information and support please follow: http://www.q-chem.com
Q-Chem developers Wiki: Q-Chem Trac (members only).

Energy Units Converter

This unit converter developed for fast and simple conversion between different systems of energy, wavelengths, frequency, and time units. User friendly interface is designed to simplify the conversion. The program supports more than ten different units of measurement (complete list of units in Table. 1). The converter also can be used for calculation of rate and equilibrium constants of chemical reactions.

Table 1. Units converted by UC V3.0 program
Supported Units
cm^-1	Units of frequency common in spectroscopy: s^-1= Hertz (Hz), GHz= 10⁹ Hz
GHz
s^-1 or Hz
Å	Units of wavelength common in spectroscopy (assumed refractive index is unity)
nm
µm
m
KJ	Common units of energy used in physics:
KJ/Mole
eV
KCal	Important units for chemistry: calorie and calorie per mole 1 Cal = 4.184 Joules
KCal/Mole
Hartree	Atomic units used in quantum chemistry calculations
Kelvin	Unit of temperature can be converted into thermodynamic temperature k_bT, where k_b – is Boltzmann constant
fs	Units of time: fs = 10^-15 s, ps = 10^-12 s, ns = 10^-9 s
ps
ns

Additional capabilities of the program include calculation of the equilibrium and rate constants of a chemical reaction using standard Transitional State Theory equations Eq.1 and Eq.2. Gibbs free energy of activation (ΔG_act) and Gibbs free energy of reaction (ΔG) can be set in any of units from Table 1.

Eq.1

Eq.2

Where k_eq—equilibrium constant, k_r—rate constant, k_b—Boltzmann constant, h—Planck's constant, R—universal gas constant, T—absolute temperature, ΔG—difference in free energy between considered states, ΔG_act—activation energy of the reaction. Top

Download: uc-win32-bin.zip (112KB) or use on-line version (beta test)

Financial calculator

There are three parameters to describe your car loan or mortgage: financed amount, annual percentage rate (APR), and monthly payment. The program allows you to calculate one of these parameters using other two. The program also estimates how much you will pay overall during the loan lifetime and how much you will pay in the interest. For example, before or during negotiations with car dealer you could easily calculate what APR corresponds to particular monthly payment if you know the total cost of the car. The program does not require internet connection and installation. Just save it on your computer and run. Top

Download: fincalc-win32-bin.zip (121KB)

Multi-Step Gaussian™ Output Processing

The script process output files in the format of the famous electronic structure package Gaussian™ [Ref]. If your Gaussian™ job input file contains „--Link1--“ keyword it could produce multi-step output. Our script splits up such a multi-step output file into separate parts.
How to use the script:
1. Transfer splitup.pl file to your UNIX/LINUX machine.

2. Make the script executable:
$ chmod +x splitup.pl

3. To spilt up Gaussian™ output file (e.g. myjob.out) type:
$ ./splitup.pl myjob.out

4. The script produces separate files for the each step of the job:
myjob_step1.out
myjob_step2.out
…

Download: splitup.zip (1.3KB)

Menu: