From owner-chemistry@ccl.net Tue May 28 03:24:00 2013 From: "Michel Petitjean petitjean.chiral/./gmail.com" 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 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 : > > 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" 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" 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): = 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" 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 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): =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"
Put scf=3Dqc
Only this .
Best Regards
= Kalyan
From: ceyo kullon biyonur|*|gmail.com
Sent: 28/05/2013 15:18
To: Dhar, Kalyan kumar -i= d#4im-
Subject: CCL:G: Gaussian crash without an error mess= age


Sent to CCL by: "ceyo  kullon" [biyonur|,|gmail.= com]
Hi,
While the geometry optimization is running, Gaussian crashe= s/terminates
without an error message. Final part of "population analys= is using the SCF
density", Gaussian cannot enter the Link 702 (L702.exe= ) which lead to
termination of the run? My input parameters are these f= or maltose:
#P HF Sto-3G opt(maxcycle=3D100) scf(xqc,tight,maxcycle=3D5= 12)

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):
&= nbsp;   X=3D     0.9835    Y= =3D    -1.9725    Z=3D    = ; 0.9356  Tot=3D     2.3944
Quadrupole moment = (field-independent basis, Debye-Ang):
   XX=3D  -118.2584=    YY=3D  -115.1066   ZZ=3D  -123.4383
&nb= sp;  XY=3D    -5.1190   XZ=3D  &nbs= p;  4.5866   YZ=3D    -6.0068
Traceless Q= uadrupole moment (field-independent basis, Debye-Ang):
   XX= =3D     0.6760   YY=3D    = ; 3.8279   ZZ=3D    -4.5039
   XY=3D&= nbsp;   -5.1190   XZ=3D     4.5866&= nbsp;  YZ=3D    -6.0068
Octapole moment (field-inde= pendent basis, Debye-Ang**2):
  XXX=3D    -6.6524&nb= sp; YYY=3D     5.1688  ZZZ=3D    -0= .9942  XYY=3D    13.1244
  XXY=3D   -= 53.2863  XXZ=3D    46.9203  XZZ=3D  &nbs= p; 11.3085  YZZ=3D   -10.2511
  YYZ=3D  &n= bsp;  3.9350  XYZ=3D   -20.6543
Hexadecapole moment= (field-independent basis, Debye-Ang**3):
XXXX=3D -7177.6926 YYYY=3D -2= 136.4849 ZZZZ=3D  -367.7532 XXXY=3D   -34.5968
XXXZ=3D&n= bsp;   17.7703 YYYX=3D  -186.6788 YYYZ=3D   -13.71= 90 ZZZX=3D     9.7745
ZZZY=3D    -7.= 8001 XXYY=3D -1500.3988 XXZZ=3D -1263.1324 YYZZ=3D  -454.4073
XXYZ= =3D  -145.3724 YYXZ=3D    85.0839 ZZXY=3D  &n= bsp;  1.5346
N-N=3D 2.265697458644D+03 E-N=3D-7.537126669665D+03&n= bsp; KE=3D 1.262600818345D+03
No NMR shielding tensors so no spin-rotat= ion constants.
Leave Link  601 at Tue May 28 11:22:11 2013, MaxMem= =3D  209715200 cpu:      
0.0
(E= nter 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:  &nbs= p;   
1.0


Thanks



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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" To: CCL Subject: CCL: Coordination / Solvation - Layer Message-Id: <-48745-130528153208-19910-xjgjFhMcfDCqeif7H39hEg::server.ccl.net> X-Original-From: Joseph E Maxwell 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" To: CCL Subject: CCL: Coordination / Solvation - Layer Message-Id: <-48746-130528164903-22640-EIkz6b1vTx6xnTkLNDD5Pw.@.server.ccl.net> X-Original-From: "Johannes Hachmann" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; 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.