BIOINFORMATICS REVIEW- JANUARY 2019

JANUARY 2019 VOL 5 ISSUE 1

“The saddest aspect of life right now is that science gathers knowledge faster than society gathers wisdom.�

-

Isaac Asimov

BiRTaking it to the next level

How to do molecular orbital analysis to find d-orbitals involved in bonding in an organometallic compound?

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Contents

January 2019

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Topics Editorial....

03 Software How to do molecular orbital analysis to find d-orbitals involved in bonding in an organometallic compound?

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FOUNDER TARIQ ABDULLAH EDITORIAL EXECUTIVE EDITOR TARIQ ABDULLAH FOUNDING EDITOR MUNIBA FAIZA SECTION EDITORS FOZAIL AHMAD ALTAF ABDUL KALAM MANISH KUMAR MISHRA SANJAY KUMAR PRAKASH JHA NABAJIT DAS

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BiR-Taking it to the next level: Editorial

EDITORIAL

As we dive into a new year, BiR desires to take a step forward towards the new developments and achievements. BiR has achieved a lot since the time of its existence in the form of our readers who have been a wonderful motivation for us.

Muniba Faiza

Founding Editor

Bioinformatics has become a broad field now, covering the important aspects of our lives such as drug designing and in the last three-to-four years, BiR has not only tried but succeeded in covering almost every domain of Bioinformatics including sequence analysis, structural bioinformatics, docking, phylogeny, evolution, tools, software, and so on. This coming year BiR will focus on several other facets of Bioinformatics covering a wide range of domains including cheminformatics, more articles focussing on bioinformatics programming, big data, and more tutorials regarding new software/tools.

We have received several suggestions and appreciation from our readers all over the world including some interesting topics to cater more articles about. We are currently working on the suggested topics and soon will be made accessible to all. Besides, BiR would like to welcome new authors who are interested in bioinformatics and sharing their knowledge worldwide.

Last year BiR commenced the annual listing of top Indian Bioinformaticians acknowledging our respected scientists and researchers working in the same field. This year BiR will try to arrange talkings and conferences with the bioinformaticians.

Besides, BiR hopes to introduce new projects and internships to young researchers working in the same field.

We have many miles to go which is not possible without the support of our readers, subscribers, and contributors. We are wholeheartedly thankful to all of you and wish you a very

Letters and responses: info@bioinformaticsreview.com

prosperous and happy new year with great achievements ahead.

Keep sharing and spreading knowledge.

Please share your thoughts info@bioinformaticsreview.com.

With best wishes!

EDITORIAL

Bioinformatics Review (BiR)

and

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at

SOFTWARE

How to do molecular orbital analysis to find dorbitals involved in bonding in an organometallic compound?

Image Credit: Stock Photos

“Gaussian software allows users to study molecular mechanics, ground-state semi-empirical calculations, Density functional theory (DFT), wave-function stability analysis (HT and DFT), electronic correlation, geometric optimization, vibrational frequency analysis, and so on.� tructure modeling of chemical compounds finds essential application in the field of cheminformatics. It is used to study the structural stability, metalion bonding, the presence of electrons, closed and open shell energies, the reactivity of complexes, molecular orbital analyzes, molecular mechanics, and so on. There is some software available for structural modeling of chemical compounds/complexes and the most widely used are Gaussian [1] and ORCA [2].

S

Gaussian software allows users to study molecular mechanics, ground-

state semi-empirical calculations, Density functional theory (DFT), wavefunction stability analysis (HT and DFT), electronic correlation, geometric optimization, vibrational frequency analysis, and so on.

In this tutorial, we will discuss Gaussian (G09) software and its application to perform molecular orbital analysis of a compound. This basic analysis requires an input file generated either using G09 or Avogadro. However, this tutorial will cover both the options and then finally the job will be run on G09 providing a detailed profile of orbitals in a compound/complex.

Let's prepare the input file first.

1. Preparing the input file The input file for the analysis can be generated by Gaussian itself but the coordinates need to calculated and input manually, therefore, it's easier to generate input file using Avogadro or ChemDraw and then open in Gaussian for further analysis. We will go through the steps for input file generation using both the software one by one. i) using Avogadro 

Draw molecule.

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

Go to 'Extensions' --> 'Optimize Geometry'



Go to 'Extensions' 'Gaussian...'



A window will appear as shown in Fig. 1, select the appropriate options as per your requirements. Our calculation is 'Geometry Optimization' and the other default parameters. After that, click 'Generate' and save the file as Gaussian Input Deck (.com) in the same folder.



Open the G09.



Go to 'File' --> 'Open'. Open the .com/.gjf file generated using ChemDraw/ Avogadro.

-->



A new window will appear showing different sections (Fig. 2).

"Pop" = "Full" displays information all orbitals "Pop" = Natural analysis

"NBO" Bond

#

# of

for Order

"Pop" = "None" # orbital information displayed

no is

"Pop" = "MK, CHELP, OR CHELPG" # produce charges fit to electrostatic potential (ESP) "Title Section" allows the user to enter a job name.

Fig. 2 A screenshot of Gaussian displaying different sections for job submission.

The first line is the path of the file.

Fig. 1 A screenshot showing the parameters of input file generation in Avogadro. ii) using ChemDraw 

Draw molecule.



Go to 'Calculation' --> 'MM2' (to optimize the geometry)



Save the file as a .gjf file.

2. Running the job in Gaussian (G09)

"%Section" specifies the name of checkpoint file.

"Route Section" is the main job defining section, where you can define which test you want to run. For this purpose, a specific keyword is used along with the command "Pop" explained as follows: "Pop" = "Reg" # displays HOMO-5 up to LUMO+5 orbital information

"Charge, Multipl." allows specifying the charge and spin multiplicity of the molecule separated by a space.

"Molecule specification" displays the atoms and their coordinates. These coordinates are calculated by Avogadro or ChemDraw else the user needs to calculate them manually.

That was about the input parameters, you can change them as per your requirements. Now, let's get back to our job submission. 

Since we want molecular orbital analysis including the d-orbitals, therefore, we will use Pop=Full command. So, type the following in the Route Section:

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Pop=Full FormCheck and click on 'OK' box present on the right side.

As you can see, another command FormCheck has been added. This command is used to create a file which contains the information of all molecular orbitals and can be plotted later. 

The memory is allocated suitably depending upon the configuration of your workstation.



You can see the progress in the 'Run Progress' bar, it will be changed to 'Ready to run processing start'.



Now, to execute g09 command, either

References 1.

Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman, J. R., ... & Nakatsuji, H. (2009). Gaussian 09, revision A. 1. Gaussian Inc. Wallingford CT, 27, 34.

2.

Neese, F. (2012). The ORCA program system. Wiley Interdisciplinary Reviews: Computational Molecular Science, 2(1), 73-78.

the click

on or go to 'Process' --> 'Begin Processing'. 

After that, it will prompt for the folder where you want to save your output file. Click 'Save'.



Again, you will notice that the Run progress bar has changed the status to 'C:\G09W\l1 is executing'.

This job takes a long time finish, wait until it finishes providing the output files. These files can then be used to visualize the d-orbitals. The analyzes of output results will be explained in the upcoming articles.

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