From owner-chemistry@ccl.net Thu Aug 22 07:24:00 2013
From: "sudipta sinha sudipta!A!udel.edu" <owner-chemistry : server.ccl.net>
To: CCL
Subject: CCL: gaussian09 does not give expected result when I consider charge
Message-Id: <-49099-130821222656-29253-1XBgQ1P4ALSzCYXs1TVovg : server.ccl.net>
X-Original-From: "sudipta  sinha" <sudipta. : .udel.edu>
Date: Wed, 21 Aug 2013 22:26:55 -0400


Sent to CCL by: "sudipta  sinha" [sudipta##udel.edu]
Hi,

I want to optimize a structure of isopropylphosphate. The isopropylphosphate contains -2 charge. However, when I dont consider the -2 charge then I am getting expected bond angle, bond length and dihedral angle(close to experimental observation). My input file looks like this

%chk=isopropylphosphate1.chk
%mem=4GB
%nprocshared=8
# opt b3lyp/6-31++g(d,p) geom=connectivity

B3LYP

-2 1
C 0.02563200 -1.04646600 -0.06925500
C -0.22829000 -2.45701400 -0.57448600
O 1.17729100 -0.53167300 -0.83050600
P 2.46250500 0.12547100 -0.18386700
O 3.46510700 0.58633300 -1.14869600
O 2.08982600 0.87247900 1.21037700
O 2.79203000 -0.56586700 1.24942000
H 0.28518400 -1.06389900 0.99306300
H -0.47283000 -2.45333600 -1.64068100
H -1.05360000 -2.91582800 -0.02482200
H 0.66551000 -3.06743500 -0.42440900
C -1.13753943 -0.06386962 -0.29976870
H -1.12874945 0.26680910 -1.31735129
H -2.06543956 -0.55460743 -0.09221688
H -1.02660650 0.77890229 0.35010005

1 2 1.0 3 1.0 8 1.0 12 1.0
2 9 1.0 10 1.0 11 1.0
3 4 1.5
4 5 2.0 6 1.0 7 1.0
5
6
7
8
9
10
11
12 13 1.0 14 1.0 15 1.0
13
14
15

Therefore, I want to use -2 charge but I want to get the result of neutral molecule. How can I do that.

Any suggestion will be appreciated.

Thanks in advance
Sudipta


From owner-chemistry@ccl.net Thu Aug 22 07:59:00 2013
From: "Dr. Vitaly Chaban vvchaban*_*gmail.com" <owner-chemistry[*]server.ccl.net>
To: CCL
Subject: CCL: gaussian09 does not give expected result when I consider charge
Message-Id: <-49100-130822075140-28865-S/cEgznujOrjnb/tWyX7Vw[*]server.ccl.net>
X-Original-From: "Dr. Vitaly Chaban" <vvchaban!^!gmail.com>
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Date: Thu, 22 Aug 2013 13:50:53 +0200
MIME-Version: 1.0


Sent to CCL by: "Dr. Vitaly Chaban" [vvchaban*|*gmail.com]
--089e012299c857bae904e487e91f
Content-Type: text/plain; charset=ISO-8859-1

Add two hydrogens nearby.

Dr. Vitaly V. Chaban


On Thu, Aug 22, 2013 at 4:26 AM, sudipta sinha sudipta!A!udel.edu <
owner-chemistry~~ccl.net> wrote:

>
> Sent to CCL by: "sudipta  sinha" [sudipta##udel.edu]
> Hi,
>
> I want to optimize a structure of isopropylphosphate. The
> isopropylphosphate contains -2 charge. However, when I dont consider the -2
> charge then I am getting expected bond angle, bond length and dihedral
> angle(close to experimental observation). My input file looks like this
>
> %chk=isopropylphosphate1.chk
> %mem=4GB
> %nprocshared=8
> # opt b3lyp/6-31++g(d,p) geom=connectivity
>
> B3LYP
>
> -2 1
> C 0.02563200 -1.04646600 -0.06925500
> C -0.22829000 -2.45701400 -0.57448600
> O 1.17729100 -0.53167300 -0.83050600
> P 2.46250500 0.12547100 -0.18386700
> O 3.46510700 0.58633300 -1.14869600
> O 2.08982600 0.87247900 1.21037700
> O 2.79203000 -0.56586700 1.24942000
> H 0.28518400 -1.06389900 0.99306300
> H -0.47283000 -2.45333600 -1.64068100
> H -1.05360000 -2.91582800 -0.02482200
> H 0.66551000 -3.06743500 -0.42440900
> C -1.13753943 -0.06386962 -0.29976870
> H -1.12874945 0.26680910 -1.31735129
> H -2.06543956 -0.55460743 -0.09221688
> H -1.02660650 0.77890229 0.35010005
>
> 1 2 1.0 3 1.0 8 1.0 12 1.0
> 2 9 1.0 10 1.0 11 1.0
> 3 4 1.5
> 4 5 2.0 6 1.0 7 1.0
> 5
> 6
> 7
> 8
> 9
> 10
> 11
> 12 13 1.0 14 1.0 15 1.0
> 13
> 14
> 15
>
> Therefore, I want to use -2 charge but I want to get the result of neutral
> molecule. How can I do that.
>
> Any suggestion will be appreciated.
>
> Thanks in advance
> Sudipta>
>
>

--089e012299c857bae904e487e91f
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<div dir=3D"ltr">Add two hydrogens nearby.</div><div class=3D"gmail_extra">=
<br clear=3D"all"><div><div dir=3D"ltr">Dr. Vitaly V. Chaban</div></div>
<br><br><div class=3D"gmail_quote">On Thu, Aug 22, 2013 at 4:26 AM, sudipta=
 sinha sudipta!A!<a href=3D"http://udel.edu">udel.edu</a> <span dir=3D"ltr"=
>&lt;<a href=3D"mailto:owner-chemistry~~ccl.net" target=3D"_blank">owner-che=
mistry~~ccl.net</a>&gt;</span> wrote:<br>

<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex"><br>
Sent to CCL by: &quot;sudipta =A0sinha&quot; [sudipta##<a href=3D"http://ud=
el.edu" target=3D"_blank">udel.edu</a>]<br>
Hi,<br>
<br>
I want to optimize a structure of isopropylphosphate. The isopropylphosphat=
e contains -2 charge. However, when I dont consider the -2 charge then I am=
 getting expected bond angle, bond length and dihedral angle(close to exper=
imental observation). My input file looks like this<br>


<br>
%chk=3Disopropylphosphate1.chk<br>
%mem=3D4GB<br>
%nprocshared=3D8<br>
# opt b3lyp/6-31++g(d,p) geom=3Dconnectivity<br>
<br>
B3LYP<br>
<br>
-2 1<br>
C 0.02563200 -1.04646600 -0.06925500<br>
C -0.22829000 -2.45701400 -0.57448600<br>
O 1.17729100 -0.53167300 -0.83050600<br>
P 2.46250500 0.12547100 -0.18386700<br>
O 3.46510700 0.58633300 -1.14869600<br>
O 2.08982600 0.87247900 1.21037700<br>
O 2.79203000 -0.56586700 1.24942000<br>
H 0.28518400 -1.06389900 0.99306300<br>
H -0.47283000 -2.45333600 -1.64068100<br>
H -1.05360000 -2.91582800 -0.02482200<br>
H 0.66551000 -3.06743500 -0.42440900<br>
C -1.13753943 -0.06386962 -0.29976870<br>
H -1.12874945 0.26680910 -1.31735129<br>
H -2.06543956 -0.55460743 -0.09221688<br>
H -1.02660650 0.77890229 0.35010005<br>
<br>
1 2 1.0 3 1.0 8 1.0 12 1.0<br>
2 9 1.0 10 1.0 11 1.0<br>
3 4 1.5<br>
4 5 2.0 6 1.0 7 1.0<br>
5<br>
6<br>
7<br>
8<br>
9<br>
10<br>
11<br>
12 13 1.0 14 1.0 15 1.0<br>
13<br>
14<br>
15<br>
<br>
Therefore, I want to use -2 charge but I want to get the result of neutral =
molecule. How can I do that.<br>
<br>
Any suggestion will be appreciated.<br>
<br>
Thanks in advance<br>
Sudipta<br>
<br>
<br>
<br>
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From owner-chemistry@ccl.net Thu Aug 22 08:55:01 2013
From: "Laidig, Bill laidig.wd]_[pg.com" <owner-chemistry_._server.ccl.net>
To: CCL
Subject: CCL: Least Median Squares
Message-Id: <-49101-130822084746-5655-hEB99NJTILi2NMW/jy0j9Q_._server.ccl.net>
X-Original-From: "Laidig, Bill" <laidig.wd[]pg.com>
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Date: Thu, 22 Aug 2013 12:47:30 +0000
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Sent to CCL by: "Laidig, Bill" [laidig.wd||pg.com]
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Hi John,

This is not exactly what you are looking for but the LMS algorithm is at th=
e heart of Rousseeuw and Leroy's Robust Regression method (an outlier insen=
sitive least squares technique):

Rousseeuw, P.J., and Leroy, A.M. (1987) Robust Regression and Outlier Detec=
tion, Wiley. New York.

They include a fortran program called PROGRESS.  I located this on the web =
at http://ftp.uni-bayreuth.de/math/statlib/general/progress . Not sure of t=
he copyright status.

I also found some other robust regression fortran codes at http://www.nehu-=
economics.info/robust-regression.html.

Bill

> From: owner-chemistry+laidig.wd=3D=3Dpg.com%a%ccl.net [mailto:owner-chemistry=
+laidig.wd=3D=3Dpg.com%a%ccl.net] On Behalf Of John McKelvey jmmckel]=3D[gmai=
l.com
Sent: Wednesday, August 21, 2013 2:56 PM
To: Laidig, Bill
Subject: CCL: Least Median Squares

Hello..
I am trying to understand some UV-VIS data and I would like to use a fortra=
n (sorry..) "all-possible-subset" least squares code as a basis for writing=
 a Least Median Squares code.  Can anyone point me to a source code for all=
-possible-subsets?
Many thanks..
John

--
John McKelvey
10819 Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel^-^gmail.com<mailto:jmmckel%5e-%5egmail.com>

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<p class=3D"MsoNormal">Hi John,<o:p></o:p></p>
<p class=3D"MsoNormal"><o:p>&nbsp;</o:p></p>
<p class=3D"MsoNormal">This is not exactly what you are looking for but the=
 LMS algorithm is at the heart of Rousseeuw and Leroy&#8217;s Robust Regres=
sion method (an outlier insensitive least squares technique):<o:p></o:p></p=
>
<p class=3D"MsoNormal"><o:p>&nbsp;</o:p></p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:&quot;Ca=
libri&quot;,&quot;sans-serif&quot;;color:#1F497D"></span>Rousseeuw, P.J., a=
nd Leroy, A.M. (1987)
<i>Robust Regression and Outlier Detection</i>, Wiley. New York.<o:p></o:p>=
</p>
<p class=3D"MsoNormal"><o:p>&nbsp;</o:p></p>
<p class=3D"MsoNormal">They include a fortran program called PROGRESS.&nbsp=
; I located this on the web at
<a href=3D"http://ftp.uni-bayreuth.de/math/statlib/general/progress">http:/=
/ftp.uni-bayreuth.de/math/statlib/general/progress</a> . Not sure of the co=
pyright status.<o:p></o:p></p>
<p class=3D"MsoNormal"><o:p>&nbsp;</o:p></p>
<p class=3D"MsoNormal">I also found some other robust regression fortran co=
des at <a href=3D"http://www.nehu-economics.info/robust-regression.html">
http://www.nehu-economics.info/robust-regression.html</a>.<o:p></o:p></p>
<p class=3D"MsoNormal"><o:p>&nbsp;</o:p></p>
<p class=3D"MsoNormal">Bill<span style=3D"font-size:11.0pt;font-family:&quo=
t;Calibri&quot;,&quot;sans-serif&quot;;color:#1F497D"><o:p></o:p></span></p=
>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:&quot;Ca=
libri&quot;,&quot;sans-serif&quot;;color:#1F497D"><o:p>&nbsp;</o:p></span><=
/p>
<p class=3D"MsoNormal"><b><span style=3D"font-size:10.0pt;font-family:&quot=
;Tahoma&quot;,&quot;sans-serif&quot;">From:</span></b><span style=3D"font-s=
ize:10.0pt;font-family:&quot;Tahoma&quot;,&quot;sans-serif&quot;"> owner-ch=
emistry&#43;laidig.wd=3D=3Dpg.com%a%ccl.net [mailto:owner-chemistry&#43;laidi=
g.wd=3D=3Dpg.com%a%ccl.net]
<b>On Behalf Of </b>John McKelvey jmmckel]=3D[gmail.com<br>
<b>Sent:</b> Wednesday, August 21, 2013 2:56 PM<br>
<b>To:</b> Laidig, Bill<br>
<b>Subject:</b> CCL: Least Median Squares<o:p></o:p></span></p>
<p class=3D"MsoNormal"><o:p>&nbsp;</o:p></p>
<div>
<div>
<div>
<div>
<p class=3D"MsoNormal" style=3D"margin-bottom:12.0pt">Hello..<o:p></o:p></p=
>
</div>
<p class=3D"MsoNormal" style=3D"margin-bottom:12.0pt">I am trying to unders=
tand some UV-VIS data and I would like to use a fortran (sorry..) &quot;all=
-possible-subset&quot; least squares code as a basis for writing a Least Me=
dian Squares code.&nbsp; Can anyone point me to a source
 code for all-possible-subsets?<o:p></o:p></p>
</div>
<p class=3D"MsoNormal" style=3D"margin-bottom:12.0pt">Many thanks..<o:p></o=
:p></p>
</div>
<p class=3D"MsoNormal">John<br clear=3D"all">
<o:p></o:p></p>
<div>
<div>
<div>
<div>
<p class=3D"MsoNormal"><br>
-- <br>
John McKelvey<br>
10819 Middleford Pl<br>
Ft Wayne, IN 46818<br>
260-489-2160<br>
<a href=3D"mailto:jmmckel%5e-%5egmail.com">jmmckel^-^gmail.com</a> <o:p></o=
:p></p>
</div>
</div>
</div>
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--_000_36CA2139DC37984ABAA757CF441D83203373064DGADCEMB025napgc_--


From owner-chemistry@ccl.net Thu Aug 22 09:29:01 2013
From: "kalyan onekalyan|a|yahoo.com" <owner-chemistry..server.ccl.net>
To: CCL
Subject: CCL:G: gaussian09 does not give expected result when I consider charge
Message-Id: <-49102-130822082944-24751-bBbNVY0lrjEARmZSWNQiIQ..server.ccl.net>
X-Original-From: kalyan <onekalyan : yahoo.com>
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Sent to CCL by: kalyan [onekalyan^yahoo.com]
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You are running bi anion. Now by following same rule you can also run neutr=
al .careful about multiplicity. If you will run this complex as a anion the=
n your charge and multiplicity will be changed too. So , these complex will=
 give you diff. Result. Now you have to select you charge and multiplicity.=
 Please read the def of Charge And multiplicity. =20

Best Regards=20
Kalyan

-----Original Message-----
> From: sudipta sinha sudipta!A!udel.edu
Sent: 22/08/2013 14:19
To: Dhar, Kalyan kumar 
Subject: CCL: gaussian09 does not give expected result when I consider char=
ge


Sent to CCL by: "sudipta  sinha" [sudipta##udel.edu]
Hi,

I want to optimize a structure of isopropylphosphate. The isopropylphosphat=
e contains -2 charge. However, when I dont consider the -2 charge then I am=
 getting expected bond angle, bond length and dihedral angle(close to exper=
imental observation). My input file looks like this

%chk=3Disopropylphosphate1.chk
%mem=3D4GB
%nprocshared=3D8
# opt b3lyp/6-31++g(d,p) geom=3Dconnectivity

B3LYP

-2 1
C 0.02563200 -1.04646600 -0.06925500
C -0.22829000 -2.45701400 -0.57448600
O 1.17729100 -0.53167300 -0.83050600
P 2.46250500 0.12547100 -0.18386700
O 3.46510700 0.58633300 -1.14869600
O 2.08982600 0.87247900 1.21037700
O 2.79203000 -0.56586700 1.24942000
H 0.28518400 -1.06389900 0.99306300
H -0.47283000 -2.45333600 -1.64068100
H -1.05360000 -2.91582800 -0.02482200
H 0.66551000 -3.06743500 -0.42440900
C -1.13753943 -0.06386962 -0.29976870
H -1.12874945 0.26680910 -1.31735129
H -2.06543956 -0.55460743 -0.09221688
H -1.02660650 0.77890229 0.35010005

1 2 1.0 3 1.0 8 1.0 12 1.0
2 9 1.0 10 1.0 11 1.0
3 4 1.5
4 5 2.0 6 1.0 7 1.0
5
6
7
8
9
10
11
12 13 1.0 14 1.0 15 1.0
13
14
15

Therefore, I want to use -2 charge but I want to get the result of neutral =
molecule. How can I do that.

Any suggestion will be appreciated.

Thanks in advance
Sudipta



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<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;">You are running bi anion. Now by following same r=
ule you can also run neutral .careful about multiplicity. If you will run t=
his complex as a anion then your charge and multiplicity will be changed to=
o. So , these complex will give you diff. Result. Now you have to select yo=
u charge and multiplicity. Please read the def of Charge And multiplicity.&=
nbsp; <br><br>Best Regards <br>Kalyan<br></div></div><hr><span style=3D"fon=
t-family: Tahoma,sans-serif; font-size: 10pt; font-weight: bold;">From: </s=
pan><span style=3D"font-family: Tahoma,sans-serif; font-size: 10pt;">sudipt=
a sinha sudipta!A!udel.edu</span><br><span style=3D"font-family: Tahoma,san=
s-serif; font-size: 10pt; font-weight: bold;">Sent: </span><span style=3D"f=
ont-family: Tahoma,sans-serif; font-size: 10pt;">22/08/2013 14:19</span><br=
><span style=3D"font-family: Tahoma,sans-serif; font-size: 10pt; font-weigh=
t: bold;">To: </span><span style=3D"font-family: Tahoma,sans-serif; font-si=
ze: 10pt;">Dhar, Kalyan kumar </span><br><span style=3D"font-family=
: Tahoma,sans-serif; font-size: 10pt; font-weight: bold;">Subject: </span><=
span style=3D"font-family: Tahoma,sans-serif; font-size: 10pt;">CCL: gaussi=
an09 does not give expected result when I consider charge</span><br><br><br=
>Sent to CCL by: "sudipta&nbsp; sinha" [sudipta##udel.edu]<br>Hi,<br><br>I =
want to optimize a structure of isopropylphosphate. The isopropylphosphate =
contains -2 charge. However, when I dont consider the -2 charge then I am g=
etting expected bond angle, bond length and dihedral angle(close to experim=
ental observation). My input file looks like this<br><br>%chk=3Disopropylph=
osphate1.chk<br>%mem=3D4GB<br>%nprocshared=3D8<br># opt b3lyp/6-31++g(d,p) =
geom=3Dconnectivity<br><br>B3LYP<br><br>-2 1<br>C 0.02563200 -1.04646600 -0=
.06925500<br>C -0.22829000 -2.45701400 -0.57448600<br>O 1.17729100 -0.53167=
300 -0.83050600<br>P 2.46250500 0.12547100 -0.18386700<br>O 3.46510700 0.58=
633300 -1.14869600<br>O 2.08982600 0.87247900 1.21037700<br>O 2.79203000 -0=
.56586700 1.24942000<br>H 0.28518400 -1.06389900 0.99306300<br>H -0.4728300=
0 -2.45333600 -1.64068100<br>H -1.05360000 -2.91582800 -0.02482200<br>H 0.6=
6551000 -3.06743500 -0.42440900<br>C -1.13753943 -0.06386962 -0.29976870<br=
>H -1.12874945 0.26680910 -1.31735129<br>H -2.06543956 -0.55460743 -0.09221=
688<br>H -1.02660650 0.77890229 0.35010005<br><br>1 2 1.0 3 1.0 8 1.0 12 1.=
0<br>2 9 1.0 10 1.0 11 1.0<br>3 4 1.5<br>4 5 2.0 6 1.0 7 1.0<br>5<br>6<br>7=
<br>8<br>9<br>10<br>11<br>12 13 1.0 14 1.0 15 1.0<br>13<br>14<br>15<br><br>=
Therefore, I want to use -2 charge but I want to get the result of neutral =
molecule. How can I do that.<br><br>Any suggestion will be appreciated.<br>=
<br>Thanks in advance<br>Sudipta<br><br><br><br>-=3D This is automatically =
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