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<p>Hello again,</p>
<p>Maybe I'm visualizing wrong, but it looks to me like the
"adsorbed" ammonia molecule did not optimize to the structure you
wanted. It looks like you have a molecule split on either side of
the graphene sheet. If this is what you meant to do, it's fine,
otherwise you need to rebuild it. It looks like you did not
re-optimize either the ammonia molecule or the graphene sheet,
which you must do if you want to have meaningful energetics. Right
now, you are seeing that starting from an extremely distorted NH3
and a distorted graphene, it is much much favorable to adsorb on
graphene, which makes sense but does not give you the information
you want.</p>
<p>Take care :)</p>
<p>Quentin<br>
</p>
<p></p>
<div class="moz-cite-prefix">On 04/03/2025 06:42, Oksana Grinevich
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:b03b5816-333c-411f-940d-2f3f5c2f742dn@googlegroups.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<blockquote type="cite"
style="color: rgb(34, 34, 34); font-family: Arial, Helvetica, sans-serif; font-size: small;">
<div>nh3_last - optimization file</div>
<div>nh3last_1 - energy for optimized geometry of bonded system</div>
<div>nh3last_3 - energy for optimized geometry of lone graphene</div>
<div>nh3G24_2 - energy of lone ammonia on a distance (imitation
of infinity distance)</div>
</blockquote>
<br>
<div class="gmail_quote">
<div dir="auto" class="gmail_attr">воскресенье, 2 марта 2025 г.
в 22:41:59 UTC+3, Quentin Pessemesse: <br>
</div>
<blockquote class="gmail_quote"
style="margin: 0 0 0 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div>Hello, <br>
</div>
<div>Could you please send the .inp files so that I can have a
look ? It looks like maybe something went wrong with the
geometry optimization of either your lone components or your
adduct.</div>
<div>Best,</div>
<div>Quentin</div>
<br>
<div class="gmail_quote">
<div dir="auto" class="gmail_attr">Le mercredi 26 février
2025 à 13:22:13 UTC+1, Oksana Grinevich a écrit :<br>
</div>
<blockquote class="gmail_quote"
style="margin:0 0 0 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">I
am running calculations to obtain binding energy of a
molecule on the graphene sheet. After obtaining the energy
value of this system (bonded), I calculate the energy
values for lone molecule and lone graphene atoms (I tried
with the same coordinates and varying them). Thus, I can
roughly find the excess (adsorption) energy as follows:
<div><br>
</div>
<div>E (excess)=E(bonded)-E(lone molecule)-E(lone
graphene)</div>
<div><br>
</div>
<div>After this step I want to convert this energy to
kJ/mol (*2625.5). It worked pretty well for benzene on
graphene (obtained 40 kJ/mol) and other aromatic
structures but for ammonia and triethylamine I can
obtain something like 700 kJ/mol or even more which
seems not physically corrected values.</div>
<div><br>
</div>
<div>I would like to know where I did wrong and what can I
do to improve results.</div>
</blockquote>
</div>
</blockquote>
</div>
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