From owner-chemistry@ccl.net Tue May 28 03:24:00 2013
From: "Michel Petitjean petitjean.chiral/./gmail.com" <owner-chemistry-#-server.ccl.net>
To: CCL
Subject: CCL: How to characterize and change the tacticity of polymer chain
Message-Id: <-48742-130528032214-4664-Xiri0SwgHEcuDv0LyT3mPA-#-server.ccl.net>
X-Original-From: Michel Petitjean <petitjean.chiral:gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Date: Tue, 28 May 2013 09:22:03 +0200
MIME-Version: 1.0
Sent to CCL by: Michel Petitjean [petitjean.chiral*o*gmail.com]
Dear Chaofu,
Having the asymmetric carbon at the origin and having fixed the
smaller substituent 1, you need to know the sense of "rotation" of 2,3,4.
The vector product 2*3 is a direct vector (non unit) to the oriented plane
defined by the vectors 2 and 3 taken in this order. If this vector product
has an acute angle with 4, the dot product 4.(2*3)=(2*3).4 is
positive, and if it
has an obtuse angle with 4, the dot product 4.(2*3)=(2.3).4 is negative.
This dot product is exactly the determinant [4,2,3]=[2,3,4] (can be
checked by hand).
Remark, unless you have a chemically impossible geometry,
the vector 1 is necessarily placed where desired,
so that the whole computation relies on 2,3,4.
Best,
Michel.
2013/5/28 WuChaofu xiaowu759,,hotmail.com <owner-chemistry(a)ccl.net>:
>
> Sent to CCL by: WuChaofu [xiaowu759[a]hotmail.com]
> Dear Michel,
> Thank you very much! You surely give such a good suggestion. However, I can not quite understand why the tacticity of polymer chains can be determined by computing the sign of determinant [2,3,4]. Could you explain it further, please?
> Yours sincerely,
> Chaofu Wu
>> ----------------------------------------
>>> Date: Mon, 27 May 2013 18:04:34 +0200
>>> Subject: Re: CCL: How to characterize and change the tacticity of polymer chain
>>> From: petitjean.chiral(a)gmail.com
>>> To: xiaowu759(a)hotmail.com
>>>
>>> Carbon is the asymmetric carbon, assumed to have coordinates (x,y,z)=(0,0,0).
>>> Best regards,
>>> Michel.
>>>
From owner-chemistry@ccl.net Tue May 28 08:34:01 2013
From: "ceyo kullon biyonur|*|gmail.com" <owner-chemistry,server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian crash without an error message
Message-Id: <-48743-130528075554-26952-WeKqKlUJS7nlRWV2KivmJQ,server.ccl.net>
X-Original-From: "ceyo kullon" <biyonur[]gmail.com>
Date: Tue, 28 May 2013 07:55:53 -0400
Sent to CCL by: "ceyo kullon" [biyonur|,|gmail.com]
Hi,
While the geometry optimization is running, Gaussian crashes/terminates
without an error message. Final part of "population analysis using the SCF
density", Gaussian cannot enter the Link 702 (L702.exe) which lead to
termination of the run? My input parameters are these for maltose:
#P HF Sto-3G opt(maxcycle=100) scf(xqc,tight,maxcycle=512)
The final part of the log file is the following:
Sum of Mulliken charges= 0.00000
Electronic spatial extent (au): <R**2>= 9449.1250
Charge= 0.0000 electrons
Dipole moment (field-independent basis, Debye):
X= 0.9835 Y= -1.9725 Z= 0.9356 Tot= 2.3944
Quadrupole moment (field-independent basis, Debye-Ang):
XX= -118.2584 YY= -115.1066 ZZ= -123.4383
XY= -5.1190 XZ= 4.5866 YZ= -6.0068
Traceless Quadrupole moment (field-independent basis, Debye-Ang):
XX= 0.6760 YY= 3.8279 ZZ= -4.5039
XY= -5.1190 XZ= 4.5866 YZ= -6.0068
Octapole moment (field-independent basis, Debye-Ang**2):
XXX= -6.6524 YYY= 5.1688 ZZZ= -0.9942 XYY= 13.1244
XXY= -53.2863 XXZ= 46.9203 XZZ= 11.3085 YZZ= -10.2511
YYZ= 3.9350 XYZ= -20.6543
Hexadecapole moment (field-independent basis, Debye-Ang**3):
XXXX= -7177.6926 YYYY= -2136.4849 ZZZZ= -367.7532 XXXY= -34.5968
XXXZ= 17.7703 YYYX= -186.6788 YYYZ= -13.7190 ZZZX= 9.7745
ZZZY= -7.8001 XXYY= -1500.3988 XXZZ= -1263.1324 YYZZ= -454.4073
XXYZ= -145.3724 YYXZ= 85.0839 ZZXY= 1.5346
N-N= 2.265697458644D+03 E-N=-7.537126669665D+03 KE= 1.262600818345D+03
No NMR shielding tensors so no spin-rotation constants.
Leave Link 601 at Tue May 28 11:22:11 2013, MaxMem= 209715200 cpu:
0.0
(Enter C:\G03W\l701.exe)
Compute integral first derivatives.
... and contract with generalized density number 0.
Leave Link 701 at Tue May 28 11:22:13 2013, MaxMem= 209715200 cpu:
1.0
Thanks
From owner-chemistry@ccl.net Tue May 28 09:54:00 2013
From: "kalyan onekalyan*yahoo.com" <owner-chemistry() server.ccl.net>
To: CCL
Subject: CCL:G: Gaussian crash without an error message
Message-Id: <-48744-130528094143-2992-4FHG/9XGMlaK78hTzvnunw() server.ccl.net>
X-Original-From: kalyan <onekalyan||yahoo.com>
Content-Type: multipart/alternative;
boundary="_D7FB75D2-5329-82FD-57C6-F55FFB1B7EAD_"
Date: Tue, 28 May 2013 15:41:29 +0200
MIME-Version: 1.0
Sent to CCL by: kalyan [onekalyan,yahoo.com]
--_D7FB75D2-5329-82FD-57C6-F55FFB1B7EAD_
Content-Transfer-Encoding: quoted-printable
Content-Type: text/plain; charset="Windows-1252"
Put scf=3Dqc
Only this .=20
Best Regards=20
Kalyan
-----Original Message-----
> From: ceyo kullon biyonur|*|gmail.com
Sent: 28/05/2013 15:18
To: Dhar, Kalyan kumar
Subject: CCL:G: Gaussian crash without an error message
Sent to CCL by: "ceyo kullon" [biyonur|,|gmail.com]
Hi,=20
While the geometry optimization is running, Gaussian crashes/terminates=20
without an error message. Final part of "population analysis using the SCF=
=20
density", Gaussian cannot enter the Link 702 (L702.exe) which lead to=20
termination of the run? My input parameters are these for maltose:=20
#P HF Sto-3G opt(maxcycle=3D100) scf(xqc,tight,maxcycle=3D512)
The final part of the log file is the following:
Sum of Mulliken charges=3D 0.00000
Electronic spatial extent (au): <R**2>=3D 9449.1250
Charge=3D 0.0000 electrons
Dipole moment (field-independent basis, Debye):
X=3D 0.9835 Y=3D -1.9725 Z=3D 0.9356 Tot=3D 2.394=
4
Quadrupole moment (field-independent basis, Debye-Ang):
XX=3D -118.2584 YY=3D -115.1066 ZZ=3D -123.4383
XY=3D -5.1190 XZ=3D 4.5866 YZ=3D -6.0068
Traceless Quadrupole moment (field-independent basis, Debye-Ang):
XX=3D 0.6760 YY=3D 3.8279 ZZ=3D -4.5039
XY=3D -5.1190 XZ=3D 4.5866 YZ=3D -6.0068
Octapole moment (field-independent basis, Debye-Ang**2):
XXX=3D -6.6524 YYY=3D 5.1688 ZZZ=3D -0.9942 XYY=3D 13.124=
4
XXY=3D -53.2863 XXZ=3D 46.9203 XZZ=3D 11.3085 YZZ=3D -10.251=
1
YYZ=3D 3.9350 XYZ=3D -20.6543
Hexadecapole moment (field-independent basis, Debye-Ang**3):
XXXX=3D -7177.6926 YYYY=3D -2136.4849 ZZZZ=3D -367.7532 XXXY=3D -34.596=
8
XXXZ=3D 17.7703 YYYX=3D -186.6788 YYYZ=3D -13.7190 ZZZX=3D 9.774=
5
ZZZY=3D -7.8001 XXYY=3D -1500.3988 XXZZ=3D -1263.1324 YYZZ=3D -454.407=
3
XXYZ=3D -145.3724 YYXZ=3D 85.0839 ZZXY=3D 1.5346
N-N=3D 2.265697458644D+03 E-N=3D-7.537126669665D+03 KE=3D 1.262600818345D=
+03
No NMR shielding tensors so no spin-rotation constants.
Leave Link 601 at Tue May 28 11:22:11 2013, MaxMem=3D 209715200 cpu: =
=20
0.0
(Enter C:\G03W\l701.exe)
Compute integral first derivatives.
... and contract with generalized density number 0.
Leave Link 701 at Tue May 28 11:22:13 2013, MaxMem=3D 209715200 cpu: =
=20
1.0
Thanks
-=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt--_D7FB75D2-5329-82FD-57C6-F55FFB1B7EAD_
Content-Transfer-Encoding: quoted-printable
Content-Type: text/html; charset="Windows-1252"
<html><head><meta content=3D"text/html; charset=3Dwindows-1252" http-equiv=
=3D"Content-Type"></head><body><div><div style=3D"font-family: Calibri,sans=
-serif; font-size: 11pt;">Put scf=3Dqc<br>Only this . <br>Best Regards <br>=
Kalyan<br></div></div><hr><span style=3D"font-family: Tahoma,sans-serif; fo=
nt-size: 10pt; font-weight: bold;">From: </span><span style=3D"font-family:=
Tahoma,sans-serif; font-size: 10pt;">ceyo kullon biyonur|*|gmail.com</span=
><br><span style=3D"font-family: Tahoma,sans-serif; font-size: 10pt; font-w=
eight: bold;">Sent: </span><span style=3D"font-family: Tahoma,sans-serif; f=
ont-size: 10pt;">28/05/2013 15:18</span><br><span style=3D"font-family: Tah=
oma,sans-serif; font-size: 10pt; font-weight: bold;">To: </span><span style=
=3D"font-family: Tahoma,sans-serif; font-size: 10pt;">Dhar, Kalyan kumar -i=
d#4im-</span><br><span style=3D"font-family: Tahoma,sans-serif; font-size: =
10pt; font-weight: bold;">Subject: </span><span style=3D"font-family: Tahom=
a,sans-serif; font-size: 10pt;">CCL:G: Gaussian crash without an error mess=
age</span><br><br><br>Sent to CCL by: "ceyo kullon" [biyonur|,|gmail.=
com]<br>Hi, <br>While the geometry optimization is running, Gaussian crashe=
s/terminates <br>without an error message. Final part of "population analys=
is using the SCF <br>density", Gaussian cannot enter the Link 702 (L702.exe=
) which lead to <br>termination of the run? My input parameters are these f=
or maltose: <br>#P HF Sto-3G opt(maxcycle=3D100) scf(xqc,tight,maxcycle=3D5=
12)<br><br>The final part of the log file is the following:<br><br> Sum of =
Mulliken charges=3D 0.00000<br> Electronic spatial extent (au):=
<R**2>=3D 9449.1250<br> Charge=3D  =
; 0.0000 electrons<br> Dipole moment (field-independent basis, Debye):<br>&=
nbsp; X=3D 0.9835 Y=
=3D -1.9725 Z=3D  =
; 0.9356 Tot=3D 2.3944<br> Quadrupole moment =
(field-independent basis, Debye-Ang):<br> XX=3D -118.2584=
YY=3D -115.1066 ZZ=3D -123.4383<br>&nb=
sp; XY=3D -5.1190 XZ=3D &nbs=
p; 4.5866 YZ=3D -6.0068<br> Traceless Q=
uadrupole moment (field-independent basis, Debye-Ang):<br> XX=
=3D 0.6760 YY=3D  =
; 3.8279 ZZ=3D -4.5039<br> XY=3D&=
nbsp; -5.1190 XZ=3D 4.5866&=
nbsp; YZ=3D -6.0068<br> Octapole moment (field-inde=
pendent basis, Debye-Ang**2):<br> XXX=3D -6.6524&nb=
sp; YYY=3D 5.1688 ZZZ=3D -0=
.9942 XYY=3D 13.1244<br> XXY=3D -=
53.2863 XXZ=3D 46.9203 XZZ=3D &nbs=
p; 11.3085 YZZ=3D -10.2511<br> YYZ=3D &n=
bsp; 3.9350 XYZ=3D -20.6543<br> Hexadecapole moment=
(field-independent basis, Debye-Ang**3):<br> XXXX=3D -7177.6926 YYYY=3D -2=
136.4849 ZZZZ=3D -367.7532 XXXY=3D -34.5968<br> XXXZ=3D&n=
bsp; 17.7703 YYYX=3D -186.6788 YYYZ=3D -13.71=
90 ZZZX=3D 9.7745<br> ZZZY=3D -7.=
8001 XXYY=3D -1500.3988 XXZZ=3D -1263.1324 YYZZ=3D -454.4073<br> XXYZ=
=3D -145.3724 YYXZ=3D 85.0839 ZZXY=3D &n=
bsp; 1.5346<br> N-N=3D 2.265697458644D+03 E-N=3D-7.537126669665D+03&n=
bsp; KE=3D 1.262600818345D+03<br> No NMR shielding tensors so no spin-rotat=
ion constants.<br> Leave Link 601 at Tue May 28 11:22:11 2013, MaxMem=
=3D 209715200 cpu: <br>0.0<br> (E=
nter C:\G03W\l701.exe)<br> Compute integral first derivatives.<br> ... and =
contract with generalized density number 0.<br> Leave Link 701 =
at Tue May 28 11:22:13 2013, MaxMem=3D 209715200 cpu: &nbs=
p; <br>1.0<br><br><br>Thanks<br><br><br><br>-=3D This is =
automatically added to each message by the mailing script =3D-<br>To recove=
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--_D7FB75D2-5329-82FD-57C6-F55FFB1B7EAD_--
From owner-chemistry@ccl.net Tue May 28 15:52:00 2013
From: "Joseph E Maxwell jaymax36|gmail.com" <owner-chemistry::server.ccl.net>
To: CCL
Subject: CCL: Coordination / Solvation - Layer
Message-Id: <-48745-130528153208-19910-xjgjFhMcfDCqeif7H39hEg::server.ccl.net>
X-Original-From: Joseph E Maxwell <jaymax36[*]gmail.com>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset=windows-1252; format=flowed
Date: Tue, 28 May 2013 12:31:56 -0700
MIME-Version: 1.0
Sent to CCL by: Joseph E Maxwell [jaymax36=gmail.com]
Hi List,
Does anyone know if there are any programs available to simulate the
coordination layer(s) of say the first and second aqueous solvation
layer around a molecule. Say, a medium size organic molecule ~ 50 - 190
Daltons, hydrophobic, apolar, polar would also be of particular interest.
Thanks
From owner-chemistry@ccl.net Tue May 28 16:51:00 2013
From: "Johannes Hachmann jh _ chemistry.harvard.edu" <owner-chemistry.@.server.ccl.net>
To: CCL
Subject: CCL: Coordination / Solvation - Layer
Message-Id: <-48746-130528164903-22640-EIkz6b1vTx6xnTkLNDD5Pw.@.server.ccl.net>
X-Original-From: "Johannes Hachmann" <jh~!~chemistry.harvard.edu>
Content-Language: en-us
Content-Transfer-Encoding: 7bit
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charset="us-ascii"
Date: Tue, 28 May 2013 16:49:00 -0400
MIME-Version: 1.0
Sent to CCL by: "Johannes Hachmann" [jh**chemistry.harvard.edu]
Hi Joseph,
That is a typical problem for an MD simulation (maybe even CPMD/AIMD,
although that's gonna be pretty tough). There are any number of possible
codes for this. Check out the following links for starters.
http://en.wikipedia.org/wiki/Molecular_dynamics
http://en.wikipedia.org/wiki/List_of_software_for_molecular_mechanics_modeli
ng
Note, that these simulations, in particular if they involve water (cf.
hydrogen-bonding, tunneling effects,...) are not trivial.
Best wishes and good luck
Johannes
-----------------------------------------------
Dr. Johannes Hachmann
Research Associate
Harvard University
Department of Chemistry and Chemical Biology
12 Oxford St, Rm M104A
Cambridge, MA 02138
-----------------------------------------------
> -----Original Message-----
> From: owner-chemistry+jh==chemistry.harvard.edu|,|ccl.net [mailto:owner-
> chemistry+jh==chemistry.harvard.edu|,|ccl.net] On Behalf Of Joseph E Maxwell
> jaymax36|gmail.com
> Sent: Tuesday, 28 May, 2013 15:32
> To: Hachmann, Johannes
> Subject: CCL: Coordination / Solvation - Layer
>
>
> Sent to CCL by: Joseph E Maxwell [jaymax36=gmail.com] Hi List,
>
> Does anyone know if there are any programs available to simulate the
> coordination layer(s) of say the first and second aqueous solvation layer
around
> a molecule. Say, a medium size organic molecule ~ 50 - 190 Daltons,
> hydrophobic, apolar, polar would also be of particular interest.
>
> ThanksTo
> recover the email address of the author of the message, please change the
> strange characters on the top line to the |,| sign. You can also look up the
X-
> Original-From: line in the mail header.