From owner-chemistry@ccl.net Mon May 9 07:20:00 2022 From: "Mozhy Mohammed mozhdehmohammadpour[]gmail.com" To: CCL Subject: CCL: imaginary frequency for a more stable structure: zwitterion CPCM solv. Message-Id: <-54663-220509071821-1073-XXYpgHY34NAHAtitNRpfkA__server.ccl.net> X-Original-From: "Mozhy Mohammed" Date: Mon, 9 May 2022 07:18:19 -0400 Sent to CCL by: "Mozhy Mohammed" [mozhdehmohammadpour^^gmail.com] Hello everyone, I have done a potential energy surface scan manually and automatically to see what's going on in the energy landscape of Zwitterion ion glycine (NH3-CH2- COO) adsorbed on a very small gold cluster (Au2) using the CPCM solvent model. My intention was to see how is the orientation of the Hydrogen of the amine group toward carboxylic oxygen which is bonded to gold (Au-Au....OCO-CH2- NH3). When I change a dihedral angle to rotate the NH3 from 0.0 to 120 with steps of 5 degrees, and don't allow the system to relax (single point frequency calculation), it seems that from 15 degrees to 55, the system decrease energy. The 30 degrees is the most stable structure and then again energy rises up to 55 degrees and doesn't show any imaginary frequency. After 55 degrees, I have got negative frequencies. However, when I allow the system to relax in each step, it goes lower in the energy but gives me 2 imaginary frequencies up to -270 cm-1 for the minimum structure. Interestingly this imaginary frequency relates to the NH3 rotation!! in summary (single point frequency calculations): 0.0 - 15 degrees: imaginary frequencies 15 - 55 degrees: no imaginary frequencies (with 30 degrees is the most stable structure) 55 - 120 degrees: imaginary frequencies I wonder how come systems decrease in energy (with respect to the single point structure) but show negative frequencies. for example, the 30 degrees optimized to 27 degrees, energy decrease but I got two imaginary frequencies up to -264 and -68 cm-1. Does it have anything to do with the CPCM implicit solvent? Kindest regards, Mozhy From owner-chemistry@ccl.net Mon May 9 11:20:01 2022 From: "Jan Labanowski jkl^wowway.biz" To: CCL Subject: CCL: Some bad news ahead for CCL Message-Id: <-54664-220509111513-11269-aaIMytGuaHelbSQIOhJNww{}server.ccl.net> X-Original-From: "Jan Labanowski" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Mon, 09 May 2022 11:15:06 -0400 MIME-Version: 1.0 Sent to CCL by: "Jan Labanowski" [jkl_-_wowway.biz] Dear CCL Members, There are problems ahead for CCL operation. My business internet provider outsourced its business services to another company. The issue is that CCL operated from a regular subnet of a small range of IP addresses. This allowed me to control access efficiently on my firewall. Instead, I will need to move the CCL to a humongous subnet that I do not control. In this subnet I will have 4 usable static IP addresses. This will require that I completely redo the firewall rules. Moreover, I do not know "who" are my neighbors on this subnet. I am not sure how my digital certificates will perform under the new IP addresses. The DNS rules will need to be either outsourced or completely rewritten. The last time I was messing with firewall rules and DNS was over 10 years ago, so it will be a learning process for me after all these years. If I cannot make CCL secure, it will be a demise of this forum in the current form. I may be forced to restrict the CCL to Web based forum only and possibly migrate it to "cloud". And the cloud is occupied in large part by spammers and crackers. So expect a lot of downtime, changes and experiments. Sorry about it, but it was not my idea. Jan Labanowski CCL Manager jkl/a\wowway.biz , ccl/a\ccl.net From owner-chemistry@ccl.net Mon May 9 11:55:00 2022 From: "Igors Mihailovs igorsm(!)cfi.lu.lv" To: CCL Subject: CCL: =?US-ASCII?Q?=5BCCL=5DRe=3A_CCL=3A_imaginary_frequency_for_a_mo?= =?US-ASCII?Q?re_stable_structure=3A_zwitterion_CPCM_solv=2E?= Message-Id: <-54665-220509094217-27120-lh9FDXCUFRGoU9H75lzgPA .. server.ccl.net> X-Original-From: Igors Mihailovs Content-Transfer-Encoding: 7bit Content-Type: multipart/alternative; boundary=----244WWU2TSN3PPCEBXENU4XNUSX3J8C Date: Mon, 09 May 2022 16:42:00 +0300 MIME-Version: 1.0 Sent to CCL by: Igors Mihailovs [igorsm- -cfi.lu.lv] ------244WWU2TSN3PPCEBXENU4XNUSX3J8C Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear Mozhy, If I understood it correctly, *within* the scan the points at 0--15 degree= s are higher in energy than the one at 30 degrees, right? If this is the case, then I think You should not be surprised because the = single point calculations are all non-optimal (and not realistic enough, it= seems)=2E More so with the single-point frequency calculations: if You are= not at the minimum on the PES, the frequency calculation is essentially me= aningless because it uses the harmonic oscillator approximation which assum= es parabolic shape of the PES -- not really what You will find far from the= minimum in most cases=2E Best regards, Igors On May 9, 2022 2:18:19 PM GMT+03:00, "Mozhy Mohammed mozhdehmohammadpour[]= gmail=2Ecom" wrote: > >Sent to CCL by: "Mozhy Mohammed" [mozhdehmohammadpour^^gmail=2Ecom] >Hello everyone, > >I have done a potential energy surface scan manually and automatically to= see=20 >what's going on in the energy landscape of Zwitterion ion glycine (NH3-CH= 2- >COO) adsorbed on a very small gold cluster (Au2) using the CPCM solvent= =20 >model=2E=20 >My intention was to see how is the orientation of the Hydrogen of the ami= ne=20 >group toward carboxylic oxygen which is bonded to gold (Au-Au=2E=2E=2E=2E= OCO-CH2- >NH3)=2E > >When I change a dihedral angle to rotate the NH3 from 0=2E0 to 120 with s= teps=20 >of 5 degrees, and don't allow the system to relax (single point frequency= =20 >calculation), it seems that from 15 degrees to 55, the system decrease=20 >energy=2E The 30 degrees is the most stable structure and then again ener= gy=20 >rises up to 55 degrees and doesn't show any imaginary frequency=2E After = 55=20 >degrees, I have got negative frequencies=2E=20 > >However, when I allow the system to relax in each step, it goes lower in = the=20 >energy but gives me 2 imaginary frequencies up to -270 cm-1 for the minim= um=20 >structure=2E Interestingly this imaginary frequency relates to the NH3=20 >rotation!! >in summary (single point frequency calculations): >0=2E0 - 15 degrees: imaginary frequencies >15 - 55 degrees: no imaginary frequencies (with 30 degrees is the most st= able=20 >structure) >55 - 120 degrees: imaginary frequencies > >I wonder how come systems decrease in energy (with respect to the single= =20 >point structure) but show negative frequencies=2E=20 >for example, the 30 degrees optimized to 27 degrees, energy decrease but = I=20 >got two imaginary frequencies up to -264 and -68 cm-1=2E=20 > >Does it have anything to do with the CPCM implicit solvent? > >Kindest regards, >Mozhy > > > >-=3D This is automatically added to each message by the mailing script = =3D->the strange characters on the top line to the {=} sign=2E You can also >look up the X-Original-From: line in the mail header=2E > >E-mail to subscribers: CHEMISTRY{=}ccl=2Enet or use: > http://www=2Eccl=2Enet/cgi-bin/ccl/send_ccl_message > >E-mail to administrators: CHEMISTRY-REQUEST{=}ccl=2Enet or use > http://www=2Eccl=2Enet/cgi-bin/ccl/send_ccl_message > >Subscribe/Unsubscribe:=20 > http://www=2Eccl=2Enet/chemistry/sub_unsub=2Eshtml > >Before posting, check wait time at: http://www=2Eccl=2Enet > >Job: http://www=2Eccl=2Enet/jobs=20 >Conferences: http://server=2Eccl=2Enet/chemistry/announcements/conference= s/ > >Search Messages: http://www=2Eccl=2Enet/chemistry/searchccl/index=2Eshtml > >If your mail bounces from CCL with 5=2E7=2E1 error, check: > http://www=2Eccl=2Enet/spammers=2Etxt > >RTFI: http://www=2Eccl=2Enet/chemistry/aboutccl/instructions/ > > ------244WWU2TSN3PPCEBXENU4XNUSX3J8C Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable Dear Mozhy,

If I understood it correctly, *= within* the scan the points at 0--15 degrees are higher in energy than the = one at 30 degrees, right?

If this is the case, then I think You shou= ld not be surprised because the single point calculations are all non-optim= al (and not realistic enough, it seems)=2E More so with the single-point fr= equency calculations: if You are not at the minimum on the PES, the frequen= cy calculation is essentially meaningless because it uses the harmonic osci= llator approximation which assumes parabolic shape of the PES -- not really= what You will find far from the minimum in most cases=2E

Best regar= ds,
Igors


On May 9, 2022 2:18:19 P= M GMT+03:00, "Mozhy Mohammed mozhdehmohammadpour[]gmail=2Ecom" <owner-ch= emistry{=}ccl=2Enet> wrote:

Sent to CCL by: "Mozhy  Mohammed" [=
mozhdehmohammadpour^^gmail=2Ecom]
Hello everyone,

I have done a p=
otential energy surface scan manually and automatically to see 
what's g=
oing on in the energy landscape of Zwitterion ion glycine (NH3-CH2-
COO)=
 adsorbed on a very small gold cluster (Au2) using the CPCM solvent 
mod=
el=2E 
My intention was to see how is the orientation of the Hydrogen of=
 the amine 
group toward carboxylic oxygen which is bonded to gold (Au-A=
u=2E=2E=2E=2EOCO-CH2-
NH3)=2E

When I change a dihedral angle to r=
otate the NH3 from 0=2E0 to 120 with steps 
of 5 degrees, and don't allo=
w the system to relax (single point frequency 
calculation), it seems th=
at from 15 degrees to 55, the system decrease 
energy=2E The 30 degrees =
is the most stable structure and then again energy 
rises up to 55 degre=
es and doesn't show any imaginary frequency=2E After 55 
degrees, I have=
 got negative frequencies=2E 

However, when I allow the system to re=
lax in each step, it goes lower in the 
energy but gives me 2 imaginary =
frequencies up to -270 cm-1 for the minimum 
structure=2E Interestingly =
this imaginary frequency relates to the NH3 
rotation!!
in summary (s=
ingle point frequency calculations):
0=2E0 - 15 degrees: imaginary frequ=
encies
15 - 55 degrees: no imaginary frequencies (with 30 degrees is the=
 most stable 
structure)
55 - 120 degrees: imaginary frequencies
<=
br>I wonder how come systems decrease in energy (with respect to the single=
 
point structure) but show negative frequencies=2E 
for example, the=
 30 degrees optimized to 27 degrees, energy decrease but I 
got two imag=
inary frequencies up to -264 and -68 cm-1=2E 

Does it have anything =
to do with the CPCM implicit solvent?

Kindest regards,
Mozhy
<=
br>

-=3D This is automatically added to each message by the mailing =
script =3D-
To recover the email address of the author of the message, p=
lease change
the strange characters on the top line to the {=} sign=2E You=
 can also
look up the X-Original-From: line in the mail header=2E
E-mail to subscribers: CHEMISTRY{=}ccl=2Enet or use:
      http://www=2Eccl=2Enet/cg=
i-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-R=
EQUEST{=}ccl=2Enet or use
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=2Eshtml

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Search =
Messages: http://www=2Eccl=2Enet/chemistry/searchccl/index=2Eshtml

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xt

RTFI: http://www=2Eccl=2Enet/chemistry/aboutccl/instructions/

------244WWU2TSN3PPCEBXENU4XNUSX3J8C-- From owner-chemistry@ccl.net Mon May 9 23:15:01 2022 From: "David Mannock dmannock~~yahoo.com" To: CCL Subject: CCL: Some bad news ahead for CCL Message-Id: <-54666-220509230806-31386-fsHEPFm9WwaJ/i0gKnUGVw(-)server.ccl.net> X-Original-From: David Mannock Content-Type: multipart/alternative; boundary="----=_Part_1404335_644292411.1652152074417" Date: Tue, 10 May 2022 03:07:54 +0000 (UTC) MIME-Version: 1.0 Sent to CCL by: David Mannock [dmannock###yahoo.com] ------=_Part_1404335_644292411.1652152074417 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Jan, Can your present provider provide you with a copy of the entire forum= in a portable format. ALT Are there back up methods that will allow you to= store the messages on a cloud in the meantime? David On Monday, May 9, 2022, 10:20:16 a.m. MDT, Jan Labanowski jkl^wowway.bi= z wrote: =20 =20 =20 Sent to CCL by: "Jan Labanowski" [jkl_-_wowway.biz] Dear CCL Members, There are problems ahead for CCL operation. My business internet provider outsourced its business services to another company. The issue is that CCL operated from a regular subnet of a small range of IP addresses. This allowed me to control access efficiently on my firewall. Instead, I will need to move the CCL to a humongous subnet that I do not control. In this subnet I will have 4 usable static IP addresses. This will require that I completely redo the firewall rules. Moreover, I do not know "who" are my neighbors on this subnet. I am not sure how my digital certificates will perform under the new IP addresses. The DNS rules will need to be either outsourced or completely rewritten. The last time I was messing with firewall rules and DNS was over 10 years a= go, so it will be a learning process for me after all these years. If I cannot make CCL secure, it will be a demise of this forum in the current form. I may be forced to restrict the CCL to Web based forum only and possibly migrate it to "cloud". And the cloud is occupied in large part by spammers and crackers. So expect a lot of downtime, changes and experiments. Sorry about it, but it was not my idea. Jan Labanowski CCL Manager jkl,,wowway.biz , ccl,,ccl.net -=3D This is automatically added to each message by the mailing script =3D-=C2=A0 =C2=A0 =C2=A0=C2=A0 =C2=A0 =C2=A0Subscribe/Unsubscribe:=20 =C2=A0 =C2=A0 =C2=A0Job: http://www.ccl.net/jobs=20=C2=A0 =C2=A0 =C2=A0=20 ------=_Part_1404335_644292411.1652152074417 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Jan, Can your present provid= er provide you with a copy of the entire forum in a portable format. ALT Ar= e there back up methods that will allow you to store the messages on a clou= d in the meantime? David

=20
=20
On Monday, May 9, 2022, 10:20:16 a.m. MDT, Jan Labanows= ki jkl^wowway.biz <owner-chemistry^_^ccl.net> wrote:



Sent to CC= L by: "Jan Labanowski" [jkl_-_wowway.biz]
Dear CC= L Members,

There are p= roblems ahead for CCL operation. My business internet provider
outsourced its business services to another company. The issu= e is that
CCL operated from a regular subnet of a= small range of IP addresses.
This allowed me to = control access efficiently on my firewall. Instead,
I will need to move the CCL to a humongous subnet that I do not control.=
In this subnet I will have 4 usable static IP ad= dresses.

This will req= uire that I completely redo the firewall rules. Moreover,
I do not know "who" are my neighbors on this subnet. I am not sure=
how my digital certificates will perform under t= he new IP addresses.
The DNS rules will need to b= e either outsourced or completely rewritten.
The = last time I was messing with firewall rules and DNS was over 10 years ago,<= br>
so it will be a learning process for me after all= these years. If I cannot
make CCL secure, it wil= l be a demise of this forum in the current form.
= I may be forced to restrict the CCL to Web based forum only and possibly
migrate it to "cloud". And the cloud is occupied in= large part by spammers
and crackers. So expect a= lot of downtime, changes and experiments.
Sorry = about it, but it was not my idea.

Jan Labanowski
CCL Manager
<= div dir=3D"ltr">jkl,,wowway.biz , ccl,,ccl.net


-=3D This is automatically added to each message by the mailing script = =3D-
To recover the email address of the author o= f the message, please change
the strange characte= rs on the top line to the ^_^ sign. You can also
lo= ok up the X-Original-From: line in the mail header.

E-mail to subscribers: CHEMISTRY^_^ccl.net o= r use:

E-mail to administrators: CHEMISTRY-REQUEST^_^ccl.= net or use

<= div dir=3D"ltr">
Before posting, check wait time = at: http://www.ccl.net=

------=_Part_1404335_644292411.1652152074417--