From owner-chemistry@ccl.net Sat May 19 01:09:00 2012 From: "cina foroutan canyslopus*|*yahoo.co.uk" To: CCL Subject: CCL: SN1 Transition state Message-Id: <-46934-120519010325-19949-blNRsIHn8SsQsCkCYRU5bw~!~server.ccl.net> X-Original-From: cina foroutan Content-Type: multipart/alternative; boundary="-976153366-650467998-1337403796=:85372" Date: Sat, 19 May 2012 06:03:16 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: cina foroutan [canyslopus[]yahoo.co.uk] ---976153366-650467998-1337403796=:85372 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Nguyen,=0A=0AThe hybridization of C on the first TS on the SN1 rxn pat= h might be either sp2-like or sp3 like. It depends on the relative energy o= f the reactants and the intermediate (carbocation). If the intermediate is = considerably higher in energy than the reactants, the TS must be sp2 like b= ecause according to the Hammond Postulate, the TS resembles the species whi= ch is more similar in energy to the TS. In addition, you must keep it in yo= ur mind that simulation of a reaction in solvent needs some things more tha= n SCRF models! In real reaction conditions solvent molecules can interact w= ith both carbocation and leaving group so lower the energy of TS and in par= ticular the intermediate. Accordingly, the TS would be more sp3 like. In SC= RF models you cannot simulate those interactions and their associated energ= y change.=A0=0A=0AGood luck,=0ACina=0A*************************************= **********************************************************=0ACina Foroutan-= Nejad, Ph. D.=0ASchool of Chemistry, University of Tehran,=0ATehran, Iran.= =0Ahttp://independent.academia.edu/CinaForoutanNejad=0A=0A=0A=0A___________= _____________________=0A From: Nguyen Minh Ly nguyenminhly2209---yahoo.com = =0ATo: "Foroutan-Nejad, Cina " =0ASent: Friday, 18 May 2012, 8:49=0ASubject: CCL: SN1 Transi= tion state=0A =0A=0ASent to CCL by: "Nguyen Minh Ly" [nguyenminhly2209:yaho= o.com]=0AHi all,=0AI have optimized my structure (C4H9Cl) to find SN1 trans= ition state (The =0Afirst stage). After that, I used IRC keyword to find re= action path. I think =0Athe reaction path is true=0A=0AMaybe my SN1 transit= ion state is wrong because in the first state of SN1 =0Areaction, the trans= ition state have C in C - Cl which sp3 Carbon. But in my =0Astructure, C in= C - Cl is sp2 carbon.=0APlease help me=0AI don't know how to do that. This= is my input IRC file and I think It have no =0Aproblems !=0A=0A=0A%chk=3DE= :/SN1 hoan chinh/check.chk=0A%mem=3D50MW=0A%nproc=3D1=0A# irc=3D(maxpoints= =3D200,calcfc) rhf/sto-3g* scrf=3D(solvent=3Dwater) nosymm=0Ageom=3Dconnect= ivity scf=3Dtight=0A=0ATitle Card Required=0A=0A0 1=0AC=0AC=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 1=A0 =A0 =A0 =A0 =A0 =A0 =A0 B1=0AH=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 2=A0 =A0 =A0 =A0 =A0 =A0 =A0 B2=A0 =A0 1=A0 =A0 =A0 =A0 =A0= =A0 =A0 A1=0AH=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 2=A0 =A0 =A0 =A0 =A0 =A0= =A0 B3=A0 =A0 1=A0 =A0 =A0 =A0 =A0 =A0 =A0 A2=A0 =A0 3=A0 =A0 =A0 =A0 =A0 = =A0 =A0 =0AD1=0AH=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 2=A0 =A0 =A0 =A0 =A0 = =A0 =A0 B4=A0 =A0 1=A0 =A0 =A0 =A0 =A0 =A0 =A0 A3=A0 =A0 3=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =0AD2=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 1=A0 =A0 =A0 =A0 = =A0 =A0 =A0 B5=A0 =A0 2=A0 =A0 =A0 =A0 =A0 =A0 =A0 A4=A0 =A0 4=A0 =A0 =A0 = =A0 =A0 =A0 =A0 =0AD3=0AH=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 6=A0 =A0 =A0 = =A0 =A0 =A0 =A0 B6=A0 =A0 1=A0 =A0 =A0 =A0 =A0 =A0 =A0 A5=A0 =A0 2=A0 =A0 = =A0 =A0 =A0 =A0 =A0 =0AD4=0AH=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 6=A0 =A0 = =A0 =A0 =A0 =A0 =A0 B7=A0 =A0 1=A0 =A0 =A0 =A0 =A0 =A0 =A0 A6=A0 =A0 2=A0 = =A0 =A0 =A0 =A0 =A0 =A0 =0AD5=0AH=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 6=A0 = =A0 =A0 =A0 =A0 =A0 =A0 B8=A0 =A0 1=A0 =A0 =A0 =A0 =A0 =A0 =A0 A7=A0 =A0 2= =A0 =A0 =A0 =A0 =A0 =A0 =A0 =0AD6=0AC=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 1= =A0 =A0 =A0 =A0 =A0 =A0 =A0 B9=A0 =A0 2=A0 =A0 =A0 =A0 =A0 =A0 =A0 A8=A0 = =A0 6=A0 =A0 =A0 =A0 =A0 =A0 =A0 =0AD7=0AH=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = 10=A0 =A0 =A0 =A0 =A0 =A0 B10=A0 =A0 1=A0 =A0 =A0 =A0 =A0 =A0 =A0 A9=A0 = =A0 2=A0 =A0 =A0 =A0 =A0 =A0 =A0 =0AD8=0AH=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 = 10=A0 =A0 =A0 =A0 =A0 =A0 B11=A0 =A0 1=A0 =A0 =A0 =A0 =A0 =A0 A10=A0 =A0 = 2=A0 =A0 =A0 =A0 =A0 =A0 =A0 =0AD9=0AH=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 10= =A0 =A0 =A0 =A0 =A0 =A0 B12=A0 =A0 1=A0 =A0 =A0 =A0 =A0 =A0 A11=A0 =A0 2= =A0 =A0 =A0 =A0 =A0 =A0 =0AD10=0ACl=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 1=A0 = =A0 =A0 =A0 =A0 =A0 B13=A0 =A0 2=A0 =A0 =A0 =A0 =A0 =A0 A12=A0 =A0 6=A0 = =A0 =A0 =A0 =A0 =A0 =0AD11=0A=0A=A0 B1=A0 =A0 =A0 =A0 =A0 =A0 1.47431703= =0A=A0 B2=A0 =A0 =A0 =A0 =A0 =A0 1.14686182=0A=A0 B3=A0 =A0 =A0 =A0 =A0 = =A0 1.08428105=0A=A0 B4=A0 =A0 =A0 =A0 =A0 =A0 1.08428709=0A=A0 B5=A0 = =A0 =A0 =A0 =A0 =A0 1.51651009=0A=A0 B6=A0 =A0 =A0 =A0 =A0 =A0 1.0948736= 7=0A=A0 B7=A0 =A0 =A0 =A0 =A0 =A0 1.08671207=0A=A0 B8=A0 =A0 =A0 =A0 =A0= =A0 1.08648693=0A=A0 B9=A0 =A0 =A0 =A0 =A0 =A0 1.51651863=0A=A0 B10=A0= =A0 =A0 =A0 =A0 =A0 1.08650334=0A=A0 B11=A0 =A0 =A0 =A0 =A0 =A0 1.0867030= 7=0A=A0 B12=A0 =A0 =A0 =A0 =A0 =A0 1.09487708=0A=A0 B13=A0 =A0 =A0 =A0 = =A0 =A0 2.92785823=0A=A0 A1=A0 =A0 =A0 =A0 =A0 =A0 94.54272741=0A=A0 A2= =A0 =A0 =A0 =A0 =A0 113.17487272=0A=A0 A3=A0 =A0 =A0 =A0 =A0 113.1707096= 3=0A=A0 A4=A0 =A0 =A0 =A0 =A0 120.32991518=0A=A0 A5=A0 =A0 =A0 =A0 =A0 = 105.75995343=0A=A0 A6=A0 =A0 =A0 =A0 =A0 111.06039901=0A=A0 A7=A0 =A0 = =A0 =A0 =A0 110.61649956=0A=A0 A8=A0 =A0 =A0 =A0 =A0 120.33488143=0A=A0 = A9=A0 =A0 =A0 =A0 =A0 110.61098280=0A=A0 A10=A0 =A0 =A0 =A0 =A0 111.0679= 9304=0A=A0 A11=A0 =A0 =A0 =A0 =A0 105.75784892=0A=A0 A12=A0 =A0 =A0 =A0 = =A0 76.76384792=0A=A0 D1=A0 =A0 =A0 =A0 =A0 114.35013589=0A=A0 D2=A0 = =A0 =A0 =A0 =A0 -114.34007794=0A=A0 D3=A0 =A0 =A0 =A0 =A0 -154.81170384=0A= =A0 D4=A0 =A0 =A0 =A0 =A0 =A0 94.31903244=0A=A0 D5=A0 =A0 =A0 =A0 =A0 -14= 7.66434619=0A=A0 D6=A0 =A0 =A0 =A0 =A0 -23.53114821=0A=A0 D7=A0 =A0 =A0 = =A0 =A0 178.28321748=0A=A0 D8=A0 =A0 =A0 =A0 =A0 =A0 23.60609839=0A=A0 D= 9=A0 =A0 =A0 =A0 =A0 147.74280879=0A=A0 D10=A0 =A0 =A0 =A0 =A0 -94.232371= 54=0A=A0 D11=A0 =A0 =A0 =A0 =A0 -90.83478191=0A=0A1 2 1.0 6 1.0 10 1.0=0A2= 4 1.0 5 1.0=0A3=0A4=0A5=0A6 7 1.0 8 1.0 9 1.0=0A7=0A8=0A9=0A10 11 1.0 12 1= .0 13 1.0=0A11=0A12=0A13=0A14=0A=0A=0A=0A-=3D This is automatically added t= o each message by the mailing script =3D-=0ATo recover the email address of= the author of the message, please change=0Athe strange characters on the t= op line to the :-: sign. You can also=0Alook up the X-Original-From: line in = the mail header.=0A=0A=0A= =A0 =A0 =A0=0A=0AE-mail to = administrators: CHEMISTRY-REQUEST:-:ccl.net or use=0A=A0 =A0 =A0 http://www.c= cl.net/cgi-bin/ccl/send_ccl_message=0A=0A=0A=A0 =A0 = =A0=0A=0ABefore posting, check= wait time at: http://www.ccl.net=0A=0A=0AConf= erences: http://server.ccl.net/chemistry/announcements/conferences/=0A=0ASe= arch Messages: http://www.ccl.net/chemistry/searchccl/index.shtml=0A=0AIf y= our mail bounces from CCL with 5.7.1 error, check:=0A=A0 =A0 =A0 http://www= .ccl.net/spammers.txt=0A=0ARTFI: http://www.ccl.net/chemistry/aboutccl/inst= ructions/ ---976153366-650467998-1337403796=:85372 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Nguyen,

The hybridization of C on the fi= rst TS on the SN1 rxn path might be either sp2-like or sp3 like. It depends= on the relative energy of the reactants and the intermediate (carbocation)= . If the intermediate is considerably higher in energy than the reactants, = the TS must be sp2 like because according to the Hammond Postulate, the TS = resembles the species which is more similar in energy to the TS. In additio= n, you must keep it in your mind that simulation of a reaction in solvent n= eeds some things more than SCRF models! In real reaction conditions solvent= molecules can interact with both carbocation and leaving group so lower th= e energy of TS and in particular the intermediate. Accordingly, the TS woul= d be more sp3 like. In SCRF models you cannot simulate those interactions and their associated energy change. 
Good luck,
Cina
*****************= ***************************************************************************= ***
Cina Foroutan-Nejad, Ph. D.
School of Chemistry, Un= iversity of Tehran,
Tehran, Iran.
http://independent.ac= ademia.edu/CinaForoutanNejad


= From: Nguyen Minh Ly nguyenmin= hly2209---yahoo.com <owner-chemistry:-:ccl.net>
To: "Foroutan-Nejad, Cina " <canys= lopus:-:yahoo.co.uk>
Sent: Friday, 18 May 2012, 8:49
Subjec= t: CCL: SN1 Transition state


Sent to = CCL by: "Nguyen Minh Ly" [nguyenminhly2209:yahoo.com]
Hi all,
I have = optimized my structure (C4H9Cl) to find SN1 transition state (The
first= stage). After that, I used IRC keyword to find reaction path. I think
= the reaction path is true

Maybe my SN1 transition state is wrong bec= ause in the first state of SN1
reaction, the transition state have C in= C - Cl which sp3 Carbon. But in my
structure, C in C - Cl is sp2 carbo= n.
Please help me
I don't know how to do that. This is my input IRC f= ile and I think It have no
problems !


%chk=3DE:/SN1 hoan chi= nh/check.chk
%mem=3D50MW
%nproc=3D1
# irc=3D(maxpoints=3D200,calcf= c) rhf/sto-3g* scrf=3D(solvent=3Dwater) nosymm
geom=3Dconnectivity scf= =3Dtight

Title Card Required

0 1
C
C    &nb= sp;             1          &nb= sp;   B1
H                =   2              B2    1&= nbsp;             A1
H     = ;             2        &n= bsp;     B3    1          &nbs= p;   A2    3             =
D1
H                 = 2              B4    1  =             A3    3    &n= bsp;        
D2
C        &n= bsp;         1           =   B5    2              A4    4              <= br>D3
H                  6=               B6    1  &n= bsp;           A5    2    &nbs= p;        
D4
H        &nbs= p;         6            &= nbsp; B7    1              A6&= nbsp;   2             
D5
H=                   6  &nbs= p;           B8    1     =         A7    2        &= nbsp;    
D6
C            &= nbsp;     1              B9    2              A= 8    6             
D7
= H                10    =         B10    1        =       A9    2          &n= bsp;  
D8
H              &n= bsp; 10            B11    1 =           A10    2     =        
D9
H         =       10            B12&nbs= p;   1            A11    2&nb= sp;          
D10
Cl      =           1            B13    2           = A12    6           
D11
<= br>  B1            1.47431703
 = ; B2            1.14686182
  B3&nb= sp;           1.08428105
  B4  &nbs= p;         1.08428709
  B5     = ;       1.51651009
  B6       =     1.09487367
  B7          =   1.08671207
  B8            = 1.08648693
  B9            1.516518= 63
  B10            1.08650334
&n= bsp; B11            1.08670307
  B1= 2            1.09487708
 =20 B13            2.92785823
  A1 = ;           94.54272741
  A2   =       113.17487272
  A3       = ;   113.17070963
  A4          120= .32991518
  A5          105.75995343
=   A6          111.06039901
  A7&nb= sp;         110.61649956
  A8    &n= bsp;     120.33488143
  A9        &= nbsp; 110.61098280
  A10          111.06= 799304
  A11          105.75784892
&nb= sp; A12          76.76384792
  D1 =         114.35013589
  D2     = ;     -114.34007794
  D3          -154.81170384
  D4         = ;   94.31903244
  D5          -147.6= 6434619
  D6          -23.53114821
&n= bsp; D7          178.28321748
  D8 = ;           23.60609839
  D9   =       147.74280879
  D10      &nbs= p;   -94.23237154
  D11          -90= .83478191

1 2 1.0 6 1.0 10 1.0
2 4 1.0 5 1.0
3
4
5<= br> 6 7 1.0 8 1.0 9 1.0
7
8
9
10 11 1.0 12 1.0 13 1.0
1= 1
12
13
14



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---976153366-650467998-1337403796=:85372-- From owner-chemistry@ccl.net Sat May 19 08:03:00 2012 From: "shamsa alina shamsa.pakistan ~~ yahoo.com" To: CCL Subject: CCL: reorganization energy Message-Id: <-46935-120519080016-22350-Ms/PdcpmMXkvKWOQtTzA7g(!)server.ccl.net> X-Original-From: "shamsa alina" Date: Sat, 19 May 2012 08:00:13 -0400 Sent to CCL by: "shamsa alina" [shamsa.pakistan^yahoo.com] hello , I want to confirm, shall i prepare my input file for calculation of reorganization energy of a compound(cation or anion) by just modifying charge and multiplicity from the previous output file for neutral one? or is there also any other method? please also confirm me for the method i described. Moreover how I will read the value of reorganization energy from that calculated resulted file? From owner-chemistry@ccl.net Sat May 19 10:54:00 2012 From: "John McKelvey jmmckel : gmail.com" To: CCL Subject: CCL:G: Parallel G03 on SGI Message-Id: <-46936-120519102555-16123-JgQ3z0Koi+41aPndmjrwpw=server.ccl.net> X-Original-From: John McKelvey Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 19 May 2012 10:25:49 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel-,-gmail.com] Folks, I am currently running G03 on an old(!) 64proc 32g memory SGI. Things run smoothly. Though the cpu probably 10x slower than today's Intel chips the machine is sitting there unused... so Could anyone point me to references, or voice their experience on running Gaussian codes on large numbers of SMP processors? I'm heading towards molecules of 120 atoms using 6311G* basis set for vib freq [student currently using ORCA/TZVP on Intel I7-2700, but he will graduate] ? Any updates to this SGI machine towards I7s is out of personal pockets, while dual SGI 64procs are sitting around unused. The student's OC'd I7 machine was built and paid for by him... Many thanks! John -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel^^^gmail.com From owner-chemistry@ccl.net Sat May 19 12:19:01 2012 From: "Prashant Singh Rana psrana{:}gmail.com" To: CCL Subject: CCL: How to validate the coordinates of the structure are ok or not before calculating the energy (using Espresso) Message-Id: <-46937-120519121644-5921-9zjFkHWnHDCoGJUfCmOMpw(~)server.ccl.net> X-Original-From: Prashant Singh Rana Content-Type: multipart/alternative; boundary=001636c5aab33fc45904c065fed9 Date: Sat, 19 May 2012 21:46:36 +0530 MIME-Version: 1.0 Sent to CCL by: Prashant Singh Rana [psrana . gmail.com] --001636c5aab33fc45904c065fed9 Content-Type: text/plain; charset=UTF-8 Dear All, I want to calculate the energy of Al (atoms=20), through espresso. I have the query regarding validation of the coordinates. As energy calculation is computationally time taking task, so it is better option to validate the coordinates of the structure before calculating the energy. So how to validate the coordinates of the structure. -- Thanks & Regards Prashant Singh Rana --001636c5aab33fc45904c065fed9 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear All,
I want to calculate the energy of Al (atoms=3D20), through esp= resso.
I have the query regarding validation of the coordinates.
As = energy calculation is computationally time taking task, so it is better opt= ion to validate the coordinates of the structure before calculating the ene= rgy.
So how to validate the coordinates of the structure.

<= br>--
Thanks & Regards

Prashant Singh Rana

--001636c5aab33fc45904c065fed9-- From owner-chemistry@ccl.net Sat May 19 21:13:01 2012 From: "Nancy nancy5villa[a]gmail.com" To: CCL Subject: CCL: In Silico Compound Library Search Message-Id: <-46938-120519211131-6922-pRTZMq1A7JzSbNsBeTwp0A]_[server.ccl.net> X-Original-From: Nancy Content-Type: multipart/alternative; boundary=00235452ef54cb375104c06d7619 Date: Sat, 19 May 2012 18:11:23 -0700 MIME-Version: 1.0 Sent to CCL by: Nancy [nancy5villa]~[gmail.com] --00235452ef54cb375104c06d7619 Content-Type: text/plain; charset=ISO-8859-1 Hi All, Does anyone know of a free cheminformatic service from which it's possible to narrow down a search for molecules by inputting limits on their molecular parameters, such as molecular weight or the number of hydrogen bond donors, etc? Such a resource would be of great help. Thanks in advance, Nancy --00235452ef54cb375104c06d7619 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi All,

Does anyone know of a free cheminformatic service from which= it's possible to narrow down a search for molecules by inputting limit= s on their molecular parameters, such as molecular weight or the number of = hydrogen bond donors, etc?=A0 Such a resource would be of great help.

Thanks in advance,
Nancy



--00235452ef54cb375104c06d7619--