bklet-RTC-19

Quantum Chemical Computation on
Combined (non-bonded) Molecular

Systems

S.Aravamudhan
Department of Chemistry
North Eastern hill University
SHILLONG 793022 MEGHALAYA

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Single Point Energy Calculation of Combined molecular systems
-DFT method / Quantum Chemical

Important Unit Conversion for
calculated energy of these systems

1 Hartree =627.51 Kcal/mol

DFT Energy (Hartree Units)

CH4 -40.30159338 Hypothetical
Combination
C6H6 -230.9757575
Total -271.27735084

&

10/23/2019 S. Aravamudhan Typical Combination of the two 2
RTC-19-Chem-NEHU

In this cited reference this author has reported results based on HF calculations;
the present report is calcualtions by DFT method
(in next slide)

Sankarampadi Aravamudhan, JMSE, A 2015, 5 (5-6) 181-196
https://ugc-inno-nehu.com/JMSE20150330-proofread.pdf

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CALCULATION : SETTINGS
AND OPTIONS

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Turning Turning
Point Point

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50

diff-energy

0

-50

31.0 cpu time in secs -100
29.0
27.0 5 10 15 20 -150
25.0
23.0 -200
21.0
19.0 -250
17.0 25
15.0

0

cpu time in secs -300

0 5 10 15 20 25

diff-energy 6

Graphical Plot of Tabulated data; with MS EXEL
application

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Dipole
moments -
Generated in
Combined
molecular
systems

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DM C6H6 & distance The increasing trend from 4.A⁰ up
Ch4 to 5 A⁰ requires much more
0.85710 3.070 attention than it has been given
0.77860 3.150 DM now, since when geometries do
0.59900 3.280 not change and are the same as
0.46930 3.400 0.9 that in isolated molecules is
0.34890 3.510 important. Then, how do charge
0.15700 3.740 separations give rise to net non
0.02780 4.017 zero dipole moments requires
0.05150 4.270 greater attention. Since the present
0.08470 4.504 work is intended mainly to account
0.08680 5.088 for induced magnetic fields, the
0.06220 5.490 electrical charge interactions could
0.03210 6.005 not be attended to as much in
0.01200 7.005 detail, yet.
0.00240 8.075
0.00100 10.052 0.8
0.00050 12.493
0.00050 15.054 0.7
0.00010 20.016
0.6

0.5

0.4

0.3

0.2

0.1

0.0 5 10 15 20 25
0

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In the following display the attention is on the combination :
(Formula C6H8) BENZENE C6H6 and HYDROGEN H2

Obviously a H2 molecule is smaller and hence could be simpler
to consider than CH4 in a combination.

For this combination, a distance dependence of H2 from C6H6 as
well as at a given distance from benzene an angular variation
around benzene held at a fixed orientation is possible. Results (by
the HF method) on this combination C6H8 also is reported in the
reference cited below :

In this cited reference this author has reported results based on HF calculations;
the present report is calcualtions by DFT method
(in next slide)

Sankarampadi Aravamudhan, JMSE, A 2015, 5 (5-6) 181-196
https://ugc-inno-nehu.com/JMSE20150330-proofread.pdf

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For the system C6H6 & H2 the distance variation

can be monitored along X, Y, and Z axis.

For a distance along X-axis designated as
2.0 A⁰ (H13 is at 2.0 A⁰)
3 perspectives are shown

The distance
between C and H is
so short that an
unusual bonding is
appearing in
structure editor

The unusual
bonds could
be deleted

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For a distance along Y-axis designated as 3.0 A⁰ (H13 is
at 3.0 A⁰), the following perspectives are shown

Unusual bonding The unusual
on account of bonds can be
short inter deleted
atomic distances

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For a distance along Z-axis designated as 0.0 A⁰ (H13 is
at 0.0 A⁰), the following are the image views

Several Unusual bonds can be
unusual bonds deleted
appear between
atoms due to
unusual
location of one
of the protons
(centre of the
ring)

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DFT Calculations were mostly less than a

minute CPU time jobs for the variation of
distance along X-axis (2.0 A⁰ to 30 A⁰ ),
along Y-axis (3.0 A⁰ to 30 A⁰ ) and along
Z-axis (0 A⁰ to 30 A⁰ ). Calculations were

made using the GAUSSIAN Program at

www.webmo.net Computational

Chemistry Portal. These trends are

shown in the following slides

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Variation Trends for H2 displacement along X-axis

Energy Dipole Moment

300 3.0
250
200 2.5
150
100 2.0

50 1.5
0
1.0
-50
0 0.5

0.0

-0.5

5 10 15 20 25 30 0 5 10 15 20 25 30 35

Energy Dipole Moment

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The next chart consists of three traces. First is the way the ring
current induced field varies at proton 13 varies with distance;
second trace is the way the proton 14 induced fields at proton 14
vary with distance and the third one is the variation of CPU time
with distance.

12

10

8

6

4

2

0

-2 5 10 15 20 25 30
0

proton 13 proton 14 CPU time

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Variation Trends for H2 displacement along Y-axis

160 Energy-Y Dipole Moment
140
120 10 20 30 0.8
100 Energy-Y 0.7
0.6
80 0.5
60 0.4
40 0.3
20 0.2
0.1
0 0.0
-20 -0.1
40 0 5 10 15 20 25 30 35
0
Dipole Moment

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The next chart consists of three traces. First is the way the ring
current induced field varies at proton 13 varies with distance;
second trace is the way the proton 14 induced fields at proton 14
vary with distance and the third one is the variation of CPU time
with distance.

12 5 10 15 20 25 30
10

8
6
4
2
0
-2

0

Proton 13 Proton 14 CPU time

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Variation Trends for H2 displacement along Z-axis

Energy Dipole Moment

0.6

450 0.5
350
250 0.4
150
0.3
50
-50 0.2
-150
-250 0.1
-350
5 10 15 20 25 30 0.0
0

0 5 10 15 20 25 30

Energy Dipole Moment

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The next chart consists of three traces. First is the way the
ring current induced field varies at proton 13 varies with
distance; second trace is the way the proton 14 induced fields
at proton 14 vary with distance and the third one is the
variation of CPU time with distance.

8

6

4

2

0

-2

-4

-6

-8
0 5 10 15 20 25 30

Proton 13 Proton 14 CPU time secs

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After knowing the trends of Physical
properties with the variation in inter
molecular distance between C6H6 and H2 in
the combined molecules-system, the
isotropic chemical shift as obtainable in
Proton NMR liquid media can be examined
for a consistency of the with the trends in the
physical properties. The NMR spectra to be
displayed are obtained by plotting the
calculated intensity vs proton chemical
shifts, and is independent of experimental
spectra as of now.

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Energy

300 10 20 30
250 Energy
200
150
100

50
0

-50
0

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Energy

300 10 20 30
250 Energy
200
150
100

50
0

-50
0

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300 Energy
250
200 5 10 15 20 25 30
150 Energy
100

50
0

-50
0

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System of C6H6 & H2

Benzene
protons

Hydrogen
protons

Note the Hydrogen protons shift value

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When one tries to retrieve this coordinate information after all the atoms have
been successfully displayed on the editor, then depending on the built in
requirements for calculations in the software, the retrieved coordinates may be in
a different coordinate system but common to both molecules and in that system
once again the input geometry is retained truly as per input, but the numerical
values of coordinates could be different and may not be as easy to compare with
what was originally given as input by the researcher. While trying to interpret the
results of output after the calculation, for those chemists who use the software by
means of peripheral input/output facilities in the software, the interpretation may
not be tangible. RECONCILITION at this stage may not be as easy this might be a
discouraging trend for further efforts on getting chemical information out of
hypothetical contexts.

Crucially, even for such a combination of molecules, the Quantum
Chemical calculations would be in a common axes system in which all
the atom coordinates (of both Benzene and Hydrogen) are expressed.
Since the user would be submitting coordinate input, user would
calculate the coordinates of the two molecules with the required specific
intermolecular distance and relative orientation. The user thus
successfully imports the coordinates and the structure gets drawn and
displayed in the structure editor of the computational chemistry portal.

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What can be done to overcome diffidence due to
discouragement requires class-room lectures
supplementing point group symmetry of
molecules and the role of symmetry elements in
describing geometry, consequent electronic
structure and the way the spectroscopic
observations are determined by electronic
structure, thus guided by molecular symmetry. An
illustration of this aspect is suggested with the
C6H6 & H2 system where the H2 is placed around
the benzene ring at the same distance ( H2
located on the circumference of a circle around
benzene).

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An illustration of rotated variation of H2 location around Benzene

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Even with benzene, the symmetry is only C2v
Combined C6H6 & H2

In this case , there is only one symmetry

element : the ring plane of symmetry 

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Till now all Shielding values and NMR spectra are isotropic values as can
be measured in NMR in liquid state. Since the sytems considered are
Hypothetical, no experimental liquid state NMR spectral data would be
available. However QM calculations can be yielding the isotropic
chemical shifts and these were displayed tin thee previous slides. It is
the Shielding Tensor which has richer information for electronic
structure consequences. These have been considered and reported in
the following references (e-booklets) .

Poster-venue-booklet-ISC2020:
http://anyflip.com/ddoa/npkr/

IUPAC-PARIS-Poster-bklet:
https://www.flipsnack.com/nehuacin/iup
ac-paris-poster-bklet-pn-lo.html

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