Documentation of Geometry Optimization

2026-03-11

Abstract

This repository presents a detailed documentation of the procedure, I have performed to do the Density Functional

Theory (DFT) calculation, including geometry optimization and molecular orbital analysis of organic compound using

ORCA, Avogadro, and IBPOView on a high-performance computing (HPC) cluster. All calculations were executed on

the “Comet” HPC cluster provided by Newcastle University. The purpose of this documentation is to provide the exact

workﬂow in order to examine the electronic properties, structural properties and molecular analysis of molecular systems.

To enhance clarity, I have also attached the supporting screenshots including step-by-step procedures to have a better

understanding and easier to guide. This guide serves as a practical reference for students, researchers, and aspiring HPC

users seeking to conduct DFT-based molecular analysis on HPC platforms.

Contents

1 Introduction: 3

1.1 Background on Density Functional Theory (DFT): . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

1.2 Studied Compounds: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

2 Requirements: 4

2.1 Software Used: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4

2.2 HPC Environment: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

3 Input ﬁle Preparation: 5

3.1 Preparation of Initial Geometry Using Avogadro: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5

3.2 Level of Theory: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8

3.3 Final ORCA Input File: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9

4 Data Transfer to HPC: 10

5 ORCA Quantum Calculation: 11

5.1 Execution of ORCA Calculation : . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

5.2 Module Loading: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

5.3 Job Submission Using SLURM: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11

5.4 Geometry Optimization and Convergence Criteria: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12

5.5 Molecular Orbital Visualization: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

5.6 Transfer to Local Machine: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

6 Analyze the output ﬁle (Iboview/Avogadro): 13

6.1 Energy Database: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

6.2 HOMO–LUMO Avogadro Analysis: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13

6.3 Geometry optimization and trajectory visualization: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

6.4 Orbital Optimization in IboView: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

6.5 Comparing Obtained Energies: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16

6.6 Frequency Calculation: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

7 Now Analyzing Other Compounds: 17

7.1 Semiquinone: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17

7.2 Hydroquinone: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18

7.3 Dibromo-benzoquinone: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

7.4 Amino-benzoquinone: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19

7.5 Energy Comparison: . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20

1 Introduction:

1.1 Background on Density Functional Theory (DFT):

What is DFT calculation? Density Functional Theory (DFT) is a computational modeling method. Its a quantum mechan-

ical algorithm to showcase the electronics properties of atom and molecules. DFT helps us to understand the distribution

of electron (electron density) around the atoms or molecules. Which later on leads to energy calculation and many other

properties of any molecules. It used in Physics, Chemistry and Material Science to investigate the physical and chemical

phenomena that needs to be calculated.

Why Do We Need DFT? As we know that the behavior of a molecule depends on electron movement, its interaction

with other electron and nuclei. To theoretically describe this properties we need to solve Schr¨odinger equation, which is

very diﬃcult for other than hydrogen like atoms (more than two electron) or for systems with many electrons. Hence we

need to have computational approach to do the calculation faster and with accuracy and this is why we need DFT method.

This below is a very good for beginners Here

1.2 Studied Compounds:

In this document, I have studied ﬁve quinone-based compounds. what is quinone-based compounds? Its a class of organic

compounds that has two carbonyl groups (C = O) in a cyclic arrangement instead of (CH). Its basic structure is 1,4-

benzoquinone. Which we will study for DFT.

1. 1,4-Benzoquinone (C

) - Its knows as quinone (Q) or para-benzoquinone (slightly dense yellow crystal). It

is the parent compounds in the quinone family. Its a simple benzene with two carbonyl groups (C = O) at opposite

sites. Which can be seen in the ﬁgure.

Figure 1: 1,4-Benzoquinone

2. Semiquinone (C

(O)

)- Semiquinone (unstable) is a radical formed by undergone a one-electron reduction

reactionfrom quinone by addition of one hydrogen atom. It is an state to lead the formation of hydroquinone. can

we show the reactions as,

Figure 2: Semiquinone

3. Hydroquinone (C

(OH)

)- As the names suggest us its a structure with hydrogen monitoring the benzene. So

the two carbonyl groups (C = O) are replaced by two hydroxyl groups (C − OH). Its lighter yellow in color than

benzoquinone. It can be formed from semiquinone as showns in below reaction.

Figure 3: Hydroquinone

4. 2,3-Dibromo-1,4-benzoquinone (C

(Br)

)- It is halogen substituted derivative of 1,4-Benzoquinone, where

two bromine (Br) atoms are attached at the 2 and 3 positions of the quinone ring.

Figure 4: 2,3-Dibromo-1,4-benzoquinone

5. 2-Amino-1,4-benzoquinone (C

N O

)- When an amino (−N H

) group attached at the 2nd position of the

quinone ring.

Figure 5: 2-Animo-1,4-benzoquinone

2 Requirements:

2.1 Software Used:

Before starting of the DFT calculation, the following packages must be installed in our system. The following tools were

used in this study:

• Avogadro2 (version 1.101.0 or higher)- We will use avogadro for molecular structure building, initial geometry opti-

mization, and for the preparation of our ORCA input ﬁles. Later also be used for analysis of the output. For the

Archlinux, you can use the command to install the avogadro.

sudo pacman -S avogad ro

• IBOView- It is used for visualization of molecular orbitals, including HOMO/LUMO from ORCA output molden ﬁles.

• Multiwfn (Optional)- Well I have worked without multiwfn, so its ﬁne without it also. The other two packages will

be enough to get our results.

2.2 HPC Environment:

Accessing to a High-Performance Computing (HPC) cluster is essential for performing computationally investigation DFT

calculations. Most importantly, How to access a HPC cluster is very important. As HPC systems are restricted environments

and provided by host institutes. You need to authorized user to run jobs on HPC cluster. I have used my friend’s user id

and performed calculation on the “Comet” HPC cluster provided by Newcastle University and hence I am able to document

this all through. We connect our machine via ssh to HPC cluster and access it to perform our jobs.

Lets begin with three easy steps.

How to connect or set the Secure Shell (SSH) conﬁguration? The HPC cluster is accessed remotely from a local

machine using Secure Shell (SSH). SSH enables secure communication between the local system and the remote cluster.

There are two ways:

1. Manual ssh Connection: In this case, the user will have to manually provide the username and hostname each

time using the command.

ssh u se rname @h ostna me

2. SSH Conﬁguration File: In this case, a ssh host key can be conﬁgured using an alias. This will be deﬁned in this

path from home directory,

~/. ssh / confi g

This ﬁle speciﬁes connection details such as host alias, the username, hostname, proxyjump, and identityﬁle. This is

to enable pass-wordless login access using a ssh command. This avoids repeatedly specifying everything manually to

connect. As ssh remembers it for you and you connect using a simple alias.

3 Input ﬁle Preparation:

3.1 Preparation of Initial Geometry Using Avogadro:

1. Open a web browser, and navigate to the ’PubChem’ database and search the compound name you have to examine.

In my work, “1,4-benzoquinone” was selected as the reference molecule. It is a relatively small organic molecule,

hence its structural data are readily available in the PubChem database. PubChem provides molecular representations

in 1D (SMILES), 2D (structural formula), and 3D (Cartesian coordinates).

2. From the compound page, download the available 3D Conformer structure ﬁle (SDF format), but wait, why we need

SDF ﬁle? A SDF (Structure Data File) contains information about the 2D or 3D structure of a molecule, including

atomic coordinates and connectivity. As we are doing quantum chemical calculations, we require the 3D structure.

3. After downloading, save it in the working directory then open the downloaded SDF ﬁle in Avogadro to visualize

and verify the molecular geometry. Avogadro is a powerful molecular editor that will allows us to visualization,

modiﬁcation of molecular structures and manipulate the methods for compounds.

4. At this stage, this SDF ﬁle for benzoquinone is not yet quantum optimized, hence we will ﬁrst do the initial optimiza-

tion in Avogadro. The geometry can be checked for structural correctness before proceeding to quantum chemical

calculations.

5. Check the molecular properties: By clicking on Analyze → Properties → Molecules. Note if its showing the

correct formula.

Figure 6: Checking molecular properties in Avogadro before initial geometry optimization.

6. Force Field Pre-Optimization: Go to Extensions → Open Babel→ Conﬁgure Force Field and select universal

force ﬁeld (UFF) in force ﬁeld box.

Figure 7: Checking molecular properties in Avogadro before initial geometry optimization.

7. Geometry Optimization: Again go to Extensions → Open Babel→ Optimize Geometry. This ensures reasonable

bond lengths and angles for the DFT calculation. In my case, you can see the changed bond from 1.08 t0 1.09 between

C-H, which means Avogadro have taken care about the bond length.

Figure 8: Checking molecular properties in Avogadro before initial geometry optimization.

8. Check the molecular properties: By clicking on Analyze → Properties → Molecules. This is to conﬁrm that

change has occured and reassurance. Note down all the other informations. Note down these values (charge = 0)

and (multiplicity = 1).

9. DFT Input Preparation: To perform quantum chemical calculations on the molecule inside Avogadro. We use a

software called ORCA. Avogadro provides a built-in interface for generating ORCA input ﬁles. ORCA is a quantum

chemistry software package to run computations like geometry optimizations, vibrational frequency calculations and

electronic structure using methods like Density Functional Theory (DFT), Hartree-Fock (HF) etc.

10. To generate the input ﬁle, we click on “Input” from the top menu and select ORCA. This will open ORCA input

conﬁguration module. This let us modify some computational parameters such as basis sets, theories, methods, etc.

This is where, we use a mathematical formulas/functions to manipulate the behavior of electrons in molecules and

get our input ﬁle ready as referred in below (ﬁgure). In this work, the Basic module was used to deﬁne the level of

theory and job type for the calculations.

Figure 9: This panel allows selection of the theoretical method, basis set, job type, charge, and multiplicity for preparing

the ORCA input ﬁle.

3.2 Level of Theory:

I personally have few questions, which I will want to include here, like what is this theory? and why this matter to do a

calculation? In quantum chemical calculations, the level of theory determines how accurately the electronic structure of a

molecule is described. It consists of two main components: the exchange–correlation functional and the basis set.

1. Exchange–Correlation Functional - The left side options in the theory like B3LYP etc are the mathematical

formulas used to estimate the energy based on its electron density. Its approximate the behavior of electrons in

molecules like how electrons interact with each other.

Basis Sets - These are the right side panel in the theory like def2-SVP, cc-pVQZ etc, these are mathematical func-

tions used to describe the shape and behavior of atomic orbitals (where electrons live) and the wave functions.

but then why we have so many? Each functional has diﬀerent strengths and weaknesses and no single functional

works best for all types of molecules, because molecules vary hugely in structural and electronic behavior. If you are

interested in to learn more or have any doubts, I suggest you to look at the oﬃcial site ORCA Manual. I am applying

the functionals: B3LYP and basis set: def2-TZVP.

Figure 10: The red arrow indicates the functional and basis sets.

2. Dispersion Correction - We manually have to add dispersion correction, like D3, D3BJ, D4. They add an extra

term to the DFT calculation explicitly modeling dispersion forces. It corrects both the energies and gradients and

give us a much better analysis. In this work, the D4 dispersion correction was applied, which improves both total

energies and optimized geometries.

Solvation Model - Lastly we check the charge to be 0 and multiplicity as 1. we add water as solvation. and solvation

type as CPCM.

3.3 Final ORCA Input File:

• After deﬁning the functional (B3LYP), basis set (def2-TZVP), dispersion correction (D4), and solvation model

(CPCM, water), we have our input ﬁle ready. It should look like as shown in below example. Save it in the working

directory, with proper name (e.g., benzoquinone.inp) for submission to the HPC cluster.

[ g olu @T4 30 BENZO ] $ cat benz oqu inone . inp

# av ogadro g enerated ORCA file ( be nzo )

# C6H 4O2 | Geometry Op tim izati on | B3LYP / def2 - TZVP

! Ti ghtOpt B3LYP def2 - TZVP CPCM ( Water ) Ti ghtSCF D4

% maxcore 16384

% pal

nprocs 16

end

% output

print [ p_mos ] 1

print [ p_basis ] 2

end

* xyz 0 1

O 2.6 3564 3 0.0 0000 7 -0.000964

O -2.636388 0. 000463 0. 002694

C 1.4 1521 7 0.0 0013 4 -0.000654

C -1.415804 0. 000411 0. 001068

C -0.671293 1. 281066 0. 000296

C 0.6 7091 9 1.2 8105 3 -0.000451

C -0.671566 -1.280538 0.00012 3

C 0.6 7071 3 -1.280581 -0.000655

H -1.211943 2. 222954 0. 000499

H -1.212307 -2.222310 0.00021 0

H 1.2 1174 1 2.2 2277 5 -0.000813

H 1.2 1136 8 -2.222343 -0.001178

• Note: Sometimes, the normal optimization setting (!Opt) says the structure is ﬁnished, but it may not be perfectly

optimized. The program stops when the changes in energy and geometry become small but not extremely small. To

make the results more accurate we use tighter settings. I have replaced !Opt by !TightOPT and !TightSCF. What

does this do?

TightOPT: makes the geometry optimization stricter. It forces the program to reduce the forces on atoms even

more before stopping.

TightSCF: makes the electronic calculation stricter. It ensures the electron density is calculated more accurately.

This must look as referenced.

4 Data Transfer to HPC:

1. Open the terminal to connect to HPC cluster via ssh, type ssh , mine is “ncl comet”. which is a alias to hostname

for comet.

[ g olu @T4 30 ~] $ ssh ncl _co met

The dollar $ key on the screen shows you are inside the HPC cluster, you can type “pwd” to check your path, or type

“whoami”. it will tell your username.

2. Make a new directory using command “mkdir” (e.g. mkdir <directory name>). I have named it ‘benzo’. Now copy

the input ﬁle from your local system to this path, using below command. I have ’benzoT430’ directory in my system.

The 100% conﬁrms the successfully copying.

[ g olu @T4 30 benzo T43 0 ] $ scp ben zoqui non e . inp ncl_comet :/ mnt / nfs / home / c50074 71 / BENZO

** WARNING : conn ect ion is not using a post - quantum key exc hang e algorithm .

** This sess ion may be vulnerable to " store now , decrypt later " a ttacks .

** The serv er may need to be upgr ade d . See https :// op enss h . com / pq . html

** WARNING : conn ect ion is not using a post - quantum key exc hang e algorithm .

** This sess ion may be vulnerable to " store now , decrypt later " a ttacks .

** The serv er may need to be upgr ade d . See https :// op enss h . com / pq . html

benzo qui none . inp 100% 754 1.4 KB / s 00:00

3. Now, we know “what” we have to run, which is our input ﬁle, but “where” and “how” the calculation runs is decided

by another ﬁle called a shell script. We cant simply use the input ﬁle without assigning it a command and resources.

4. To run our DFT calculations on the HPC cluster, we need an intermediate shell script to submit our computational

jobs on clusters with speciﬁc conﬁgurations and managed resources. Once this shell script is used to connect the

’ORCA input’ ﬁle with the Comet scheduler, it implements the resources from the clusters, such as computing nodes,

CPU cores, time, etc. This ensures that the calculation is performed eﬃciently and returns the results. How does

this shells scripts looks like?

[ c5 00 7471@co me tl og in01 ( comet ) benzo ] $ cat orca - script . sh

#!/ bin / bash

# SBATCH -- account = come t_o cm fli b

# SBATCH -- partit ion = d efa ult_f ree

# SBATCH -- job - name = or ca_PD _p arall el

# SBATCH -- time = 24:00:00 # HH : MM : SS

# SBATCH -- nodes =1

# SBATCH -- ntasks =16

# SBATCH -- cpus - per - task =1

# SBATCH -- threads - per - core =1

# SBATCH -- mem =32 G

# exp ort TMPDIR =/ scratch / $ SLU RM_JO BID

export TMPDIR =/ tmp /

# exp ort PATH =/ mnt / nfs / home / c5007 471 / Pa ckages / orca / orca_6_1_0_linux_x86 -64

_s hared _o pe nmpi4 18 /: $PATH

# exp ort PATH =/ opt / sof tware / e asybuild / s oftware / Op enMP I /4.1.6 - GCC -13.2 .0/ bin : $PATH

# exp ort PATH =/ opt / sof tware / ma nual / apps / ope nmpi / 5.0. 8/ bin /: $ PATH

# exp ort L D_LIB RARY_ PA TH =/ mnt / nfs / home / c50074 71 / Pac kage s / orca / orc a_6 _1_ 0_linux_x86 -64

_s hared _o pe nmpi4 18 / lib : $ L D_ LIBRA RY _PATH

# exp ort L D_LIB RARY_ PA TH =/ opt / so ftware / easybuild / softw are / OpenMPI /4.1.6 - GCC -13.2 .0/ lib :/

opt / sof tware / ma nual / apps / ope nmpi / 5.0. 8/ lib : $ L D_L IB RARY_ PA TH

# default ones

# https :// hpc . re se ar chcom pu ting . ncl . ac . uk / dok uwik i / doku . php ? id = started : come t_res ou rces

# echo -n " This script is running on "

# uname -a

# ho stname

~/ Pac kage s / orca / orc a_6 _1_0_linux_x86 -64 _sha re d_ope nm pi 418 / orca $ {1%.*}. inp > $ {1 %.*} . out

# mpi run -np 8 / mnt / nfs / home / c50 0747 1 / Packa ges / orca / orca _6_ 1_0 _li nux _x8 6 -64

_s hared _o pe nmpi4 18 / o rc a_s ta rtup_ mp i phen2 . int . tmp ph en2

5 ORCA Quantum Calculation:

5.1 Execution of ORCA Calculation :

1. As we have all the thing to do calculation. lets run a ORCA quantum calculation using below command and save

output ﬁle.

orca be nzo quino ne . inp > benz oquin one . out

2. We get this the output ﬁle, which stores all calculated results and convergence information.

[ c5 00 7471@co me tl og in01 ( comet ) benzo ] $ orca benz oqu in one . inp > be nzoqu ino ne . out

!! !! !! !!! !! !! !! !!!!! !! !! !! !!!!! !! !! !! !!!!! !! !! !! !! !!! !! !! !! !!!!! !! !!

[ file o rca _to ols / qcsys . cpp , line 50]:

5.2 Module Loading:

1. The HPC system has many module. To get out job done, we load speciﬁc software modules named orca and OpenMPI

in current working environment using ’module load’ command. You can search the module load availability using

“module spider <name>”.

module load Open MPI

2. OpenMPI open source (Message Passing interface) is for allowing ORCA to run in parallel computing.

5.3 Job Submission Using SLURM:

1. Now using the ’sbatch’ command, which is for submitting batch jobs to the SLURM workload manager using shell

script and input ﬁle. but What is SLURM? it stands for Simple Linux Utility for Resource Management, is an open-

source job scheduler designed for Linux clusters of all sizes. It allows users to submit a job and perform computing.

sbatch orca - script . sh ben zoquinon e . inp

2. This command tells the job submission ID, which you can check by typing below command,

squeue --me

I have alias for this command to “me”. This command also speciﬁes the node, nodelisting and timing its taking to

get the job done. Once the job is completed, you wont see the time on typing ’me’. I got the below nodelisting.

[ c5 00 7471@co me tl og in01 ( comet ) benzo ] $ me

JOBID P ART ITION NAME USER ST TIME NODES N ODELIST ( REA SON )

1233642 d efa ult _f or ca_PD_ c5007 471 PD 0:00 1 ( None )

[ c5 00 7471@co me tl og in01 ( comet ) benzo ] $ me

JOBID P ART ITION NAME USER ST TIME NODES N ODELIST ( REA SON )

1233642 d efa ult _f or ca_PD_ c5007 471 R 0:10 1 compute 032

[ c5 00 7471@co me tl og in01 ( comet ) benzo ] $ me

JOBID P ART ITION NAME USER ST TIME NODES N ODELIST ( REA SON )

1233642 d efa ult _f or ca_PD_ c5007 471 R 0:28 1 compute 032

5.4 Geometry Optimization and Convergence Criteria:

1. Once the output is created, you can check the convergence message, by ﬁnding the “HURRAY” message in output

ﬁle.

.- - -- - -- --- --- --- -- - -.

-- --- -- -- --- -- --- -- -- -| Geomet ry conv erg enc e |- --- -- -- - -- -- --- -- --- -- --

Item value Tol era nce Con ver ged

-- -- --- -- -- --- -- -- --- -- -- -- --- -- -- --- -- -- --- -- -- -- --- -- -- --- -- -- --- --

Energy change -0.0 000007962 0.000 001 0000 YES

RMS gradi ent 0.000 011 9495 0.0000 300 000 YES

MAX gradi ent 0.000 045 5551 0.0001 000 000 YES

RMS step 0. 00005 446 33 0.0 00600 000 0 YES

MAX step 0. 00009 289 44 0.0 01000 000 0 YES

-- -- --- -- -- --- -- -- --- -- -- -- - -- -- -- --- -- -- --- -- -- --- -- -- -- --- -- -- --- -- -- --

.. .. .. ..... .. .. .. .. ..... .. .. .. .. ..... .. .. .. .. .. ... .. .. ..

Max ( Bonds ) 0.0000 Max ( Angles ) 0.01

Max ( Dihed ) 0.01 Max ( Improp ) 0.00

-- -- --- -- -- --- -- -- --- -- -- -- --- -- -- --- -- -- --- -- -- -- --- -- -- --- -- -- --- --

** ** ******* ** ** ** ** ** ** HURRAY ** ******* ** ** ** *****

*** THE OP TIMIZ ATI ON HAS CON VERGED ***

** ** ** ** ***** ** ** ** ** ** ***** ** ** ** ** ** ** ***** ** **

2. Try to look for all yes, but even if its not showing all yes, it tells the optimization has reached its convergence. Hence

we have obtained our geometry optimization.

Eve ryt hin g but the energy has conv erg ed . However , the energy

appears to be close enough to con ver gen ce to make sure that the

final e val uat ion at the new geo metry re pre sen ts the equ ilibrium e nergy .

Converge nce will ther efo re be signale d now

** ** ******* ** ** ** ** ** ** HURRAY ** ******* ** ** ** *****

*** THE OP TIMIZ ATI ON HAS CON VERGED ***

** ** ** ** ***** ** ** ** ** ** ***** ** ** ** ** ** ** ***** ** **

3. Incase, you found any no in ’HURRAY’. you can resubmit a job in order to get all convergence by editing the input

ﬁle.

5.5 Molecular Orbital Visualization:

1. To visualization of molecular orbitals and electron density, the ORCA wavefunction data output ﬁles is converted

into the ’Molden’ format using the “orca 2mkl” library by running command,

orc a_2 mkl benzo quino ne - molden

2. This command executes in such way below,

$ or ca_ 2mk l be nzo quino ne - mold en

Reading the input file benzo qui none . gbw ... done

Writing the output file b enzoq uin one . mol den . input ... done

The molden format ﬁle generated by this command will be studied using IboView and multiwfn.

5.6 Transfer to Local Machine:

• Now its time to scp all the datas ﬁle from HPC system directory to T430’s (local system) working directory. You

need to run scp with (-r) command using on your system’s terminal. This command will copying whole directory into

T430’s.

6 Analyze the output ﬁle (Iboview/Avogadro):

6.1 Energy Database:

1. To ﬁnd out the energy for orbital, we can have a shell script, which will print the output ﬁle energy, molden energy

value and energy gap calculation for HOMO & LUMO. Create a ﬁle, and write something as given below.

#!/ bin / sh

orc a_2 mkl $1 -molden

echo 0 | Multi wfn_n oGUI $1 . mol den . input 2 > / dev / null | grep LUMO

echo 0 | Multi wfn_n oGUI $1 . mol den . input 2 > / dev / null | grep HOMO

2. To know, the energy, we execute this script with the input, as shows in below,

[ c5 00 7471@co me tl og in01 ( comet ) BENZO ] $ h omo_lomo . sh be nzoqu ino ne

Reading the input file benzo qui none . gbw ... done

Writing the output file b enzoq uin one . mol den . input ... done

Orbital 29 is LUMO , en ergy : -0.133502 a. u. -3.632773 eV

HOMO - LUMO gap : 0 .144868 a. u. 3.942 068 eV 380 .351858 kJ / mol

Note : Or bita l 28 is HOMO , en ergy : -0.278370 a. u. -7.574842 eV

HOMO - LUMO gap : 0 .144868 a. u. 3.942 068 eV 380 .351858 kJ / mol

6.2 HOMO–LUMO Avogadro Analysis:

By opening the outﬁle ﬁle “benzoquinone.out” in avogadro ﬁle. It was examined to determine the frontier orbitals energies

obtained from the DFT calculation. The Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular

Orbital (LUMO) are important for understanding the electronic properties and chemical reactivity of the molecule. We

will focus on orbital 28 and 29 as its initial value.

• In the below ﬁgure we can see, the HOMO energy was found to be −7.574eV corresponding to orbital 28,

Figure 11: HOMO energy of benzoquinone in Avogadro.

• And, in this below ﬁgure, the LUMO energy was found to be −3.632eV corresponding to orbital 29,

Figure 12: LOMO energy of benzoquinone in Avogadro.

The HOMO–LUMO energy gap was calculated to be 3.942eV indicating the energy required for electronic excitation from

the HOMO to the LUMO.

6.3 Geometry optimization and trajectory visualization:

If you notice in the ﬁle, you will have a ﬁle like this ’benzoquinone-trj.xyz’, it is a trajectory ﬁle, which shows the molecular

structure changes over time or optimization steps. Visualization of this trajectory in Avogadro enables inspection of the

geometry optimization process and veriﬁcation of structural convergence. The animation can be watched using this link

6.4 Orbital Optimization in IboView:

IboView is used for electronic structure analysis and orbital visualization. The structural dynamics and geometry opti-

mization trajectories were visualized separately using Avogadro.

1. We import the molden ﬁle in IboView, the electronic structure obtained from DFT calculations was exported in

Molden format and analyzed. This enabled visualization of molecular orbitals and intrinsic bond orbitals, providing

insight into the bonding characteristics and electron distribution of the molecule. Note that this molden ﬁle will give

the energy values in atomic units.

2. We see orbital visualization, by clicking on ’Data sets’ and see the orbitals. On double clicking, we can see orbital

optimize structure as shows the below,

In the below ﬁgure we can see, the HOMO energy was found to be −0.278a.u., corresponding to orbital 28,

Figure 13: HOMO energy of benzoquinone in Iboview.

And, in this below ﬁgure, the LUMO energy was found to be −0.133a.u., corresponding to orbital 29,

Figure 14: LOMO energy of benzoquinone in Iboview.

The obtained HOMO–LUMO energy gap was calculated to be 0.144a.u. by molden ﬁle, indicating the energy required for

electronic excitation from the HOMO to the LUMO.

6.5 Comparing Obtained Energies:

Comparison of the molecular orbitals of benzoquinone obtained from DFT calculations using ORCA. The bottom row shows

the highest occupied molecular orbital (HOMO), and the top row shows the lowest unoccupied molecular orbital (LUMO),

visualized using Avogadro and IboView.

Figure 15: Comparison of molecular orbitals of benzoquinone obtained from DFT calculations.

We have tabulated orbital energies of benzoquinone as in the below table,

Orbital Energy (a.u.) Energy (eV)

HOMO Orbital (28) −0.278 −7.574

LUMO Orbital (29) −0.133 −3.632

HOMO–LUMO Gap 0.144 3.942

Table 1: Orbital energies of benzoquinone in atomic units and electron volts.

6.6 Frequency Calculation:

We have frequency trajectory also, which shows the intensity of IR modes at the respective wavelength with diﬀerent

intensity. You can check this by opening frequency output ﬁle in avogadro. Check this video out We can also plot the

frequency plot using the IR Spectrum data. We can have the below spectrum where the x axis is showing the wavelength

and y axis indicate the IR intensity.

7 Now Analyzing Other Compounds:

7.1 Semiquinone:

The semiquinone species represents a radical intermediate and was not available as a stable neutral structure in public

databases. Therefore, its initial geometry was constructed manually in Avogadro based on the benzoquinone framework,

followed by geometry optimization at the same level of theory. .

1. Neutral Semiquinone Radical (From benzoquinone Oxidation): Open downloaded SDF ﬁle (which is ben-

zoquinone), then change one double bond of C=O to C-O. This decides, the oxygen with radical. Semiquinone has

one unpaired electron, typically delocalized on one oxygen. In Avogadro, you don’t move the electron manually, you

just mark the molecule as ready for an open-shell calculation in DFT. Now add another hydrogen atom so you have

One OH and One O• which is raadical on oxygen. You will see the green arrow (radical indicator).

2. Check the molecular properties: By clicking on Analyze → Properties → Molecules and Atoms Properties. This

conﬁrms that a radical has been formed and tells other informations. Note the (charge =0) and (multiplicity =

2) which means one unpaired electron.

Orbital Energy (a.u.) Energy (eV)

HOMO Orbital (29) -0.212 -5.776

LUMO Orbital (30) -0.030 -0.838

HOMO–LUMO Gap 0.181 4.938

Orbital Energy (a.u.) Energy (eV)

HOMO Orbital (306) -0.258 -7.026

LUMO Orbital (307) -0.130 -3.546

HOMO–LUMO Gap 0.127 3.480

Table 2: Alpha Energy and Beta Energy

Figure 16: Conﬁrming the Molecular Properties for semiquinone.

3. Follow the same procedure from above section and do force ﬁeld pre-optimization, geometry optimization, and ORCA,

and save the input ﬁle. Later transfer to the HPC system and do calculation following the same procedure in Section

5. After the DFT calculation completes, transfer the results back to the local system and check the energy values

once on HPC system.

( OSS 2410.0) [ c 50 07 47 1@ comet lo gi n0 1 ( come t ) semi ]$ homo_lomo . sh semi

Reading the input file semi . gbw ... done

Writing the output file semi . molden . input ... done

Orbital 30 is alpha - LUMO , en ergy : -0.030827 a. u. -0.838858 eV

Orbital 307 is beta - LUMO , en ergy : -0.130328 a. u. -3.546396 eV

HOMO - LUMO gap of a lpha or bita ls : 0.1814 71 a .u . 4.9380 71 eV

HOMO - LUMO gap of beta orbit als : 0. 127890 a .u. 3. 480068 eV

Note : Or bita l 29 is alpha - HOMO , en ergy : -0.212298 a. u. -5.776930 eV

Orbital 306 is beta - HOMO , en ergy : -0.258218 a. u. -7.026464 eV

HOMO - LUMO gap of a lpha or bita ls : 0.1814 71 a .u . 4.9380 71 eV

HOMO - LUMO gap of beta orbit als : 0. 127890 a .u. 3. 480068 eV

7.2 Hydroquinone:

1. We found the energy for hydroquinone to be,

[ c5 00 7471@co me tl og in01 ( comet ) hydro ] $ h omo_lomo . sh hydro

Reading the input file hydro . gbw ... done

Writing the output file hydro . molden . input ... done

Orbital 30 is LUMO , en ergy : -0.017805 a. u. -0.484510 eV

HOMO - LUMO gap : 0 .192576 a. u. 5.240 247 eV 505 .607112 kJ / mol

Note : Or bita l 29 is HOMO , en ergy : -0.210381 a. u. -5.724757 eV

HOMO - LUMO gap : 0 .192576 a. u. 5.240 247 eV 505 .607112 kJ / mol

2. Now comparing the iboview and avogadro with their energies.

3. We have tabulated orbital energies of benzoquinone as in the below table,

Orbital Energy (a.u.) Energy (eV)

HOMO Orbital (29) -0.210 -5.724

LUMO Orbital (30) -0.017 -0.484

HOMO–LUMO Gap 0.192 5.240

Table 3: Orbital energies of hydroquinone

7.3 Dibromo-benzoquinone:

1. We got this followed energy value for dibromo benzoquinone.

[ c5 00 7471@co me tl og in01 ( comet ) bromo ] $ h omo_lomo . sh bromo

Reading the input file bromo . gbw ... done

Writing the output file bromo . molden . input ... done

Orbital 63 is LUMO , en ergy : -0.143403 a. u. -3.902201 eV

HOMO - LUMO gap : 0 .130301 a. u. 3.545 658 eV 342 .104104 kJ / mol

Note : Or bita l 62 is HOMO , en ergy : -0.273704 a. u. -7.447859 eV

HOMO - LUMO gap : 0 .130301 a. u. 3.545 658 eV 342 .104104 kJ / mol

2. Now comparing the iboview and avogadro with their energies

3. We have tabulated orbital energies of dibromo-benzoquinone as in the below table

Orbital Energy (a.u.) Energy (eV)

HOMO Orbital (62) -0.273 -7.447

LUMO Orbital (63) -0.143 -3.902

HOMO–LUMO Gap 0.130 3.545

Table 4: Orbital energies of Dibromo-benzoquinone

7.4 Amino-benzoquinone:

1. We have obtained this below energy values,

[ c5 00 7471@co me tl og in01 ( comet ) animo ] $ h omo_lomo . sh amino

Reading the input file amino . gbw ... done

Writing the output file amino . molden . input ... done

Orbital 33 is LUMO , en ergy : -0.120776 a. u. -3.286491 eV

HOMO - LUMO gap : 0 .113470 a. u. 3.087 667 eV 297 .914686 kJ / mol

Note : Or bita l 32 is HOMO , en ergy : -0.234246 a. u. -6.374158 eV

HOMO - LUMO gap : 0 .113470 a. u. 3.087 667 eV 297 .914686 kJ / mol

2. Now comparing the iboview and avogadro with their energies.

3. We have tabulated orbital energies of Amino-benzoquinone as in the below table,

Orbital Energy (a.u.) Energy (eV)

HOMO Orbital (32) -0.234 -6.374

LUMO Orbital (33) -0.120 -3.286

HOMO–LUMO Gap 0.113 3.087

Table 5: Orbital energies of Amino-benzoquinone

7.5 Energy Comparison:

The below ﬁgure show the comparative of all the energy for other compounds, its also tells the HOMO, LUMO energy

diﬀerence.

Figure 17: Comparative ﬁgures for all other compounds.