From owner-chemistry@ccl.net Fri Aug 23 01:20:00 2013 From: "sudipta sudipta.mml++gmail.com" To: CCL Subject: CCL: gaussian09 does not give expected result when I consider charge Message-Id: <-49103-130823010150-20187-OjX3q0MdmCA5hyvQBk7nPw#,#server.ccl.net> X-Original-From: sudipta Content-Type: multipart/alternative; boundary=089e013a15e63e993104e4964dbe Date: Fri, 23 Aug 2013 01:01:38 -0400 MIME-Version: 1.0 Sent to CCL by: sudipta [sudipta.mml!^!gmail.com] --089e013a15e63e993104e4964dbe Content-Type: text/plain; charset=ISO-8859-1 Hi Dr. Vitaly V. Chaban, What will be the suitable position of those two hydrogens. I tried to place two hydrogens near phosphate group but after few iteration they form bonds with phosphate oxygen. But I don't want those bonds. This is because isopropylphosphate is surrounded with counter ions in reality. However, I had tried with two sodium and one Mg2+ but they also form a bond with oxygen atom of phosphate group. Therefore, finally I placed a Mg2+ at a lager distance from the phosphate group and also put a restraint between the phosphorous and the Mg2+ ion. But, I am not sure how right is it? Any suggestion will be highly appreciated. Best Sudipta On Thu, Aug 22, 2013 at 7:50 AM, Dr. Vitaly Chaban vvchaban*_*gmail.com < owner-chemistry^-^ccl.net> wrote: > Add two hydrogens nearby. > > Dr. Vitaly V. Chaban > > > On Thu, Aug 22, 2013 at 4:26 AM, sudipta sinha sudipta!A!udel.edu _ 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** >> E-mail to subscribers: CHEMISTRY _ ccl.net or use:>> >> E-mail to administrators: CHEMISTRY-REQUEST _ ccl.net or use>> **>> >> >> > --089e013a15e63e993104e4964dbe Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi Dr. Vitaly V. Chaban,

What will be the= suitable position of those two hydrogens. I tried to place two hydrogens n= ear phosphate group but after few iteration they form bonds with phosphate = oxygen. But I don't want those bonds. This is because isopropylphosphat= e is surrounded with counter ions in reality. However, I had tried with two= sodium and one Mg2+ but they also form a bond with oxygen atom of phosphat= e group. Therefore, finally I placed a Mg2+ at a lager distance from the ph= osphate group and also put a restraint=A0 between the phosphorous and the M= g2+ ion. But, I am not sure how right is it? Any suggestion will be highly = appreciated.

Best
Sudipta

On Thu, Aug 22, 2013 at 7:50 AM, Dr. Vitaly Cha= ban vvchaban*_*gmail.com <owner-che= mistry^-^ccl.net> wrote:
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 =A0sinha" [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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--089e013a15e63e993104e4964dbe-- From owner-chemistry@ccl.net Fri Aug 23 01:54:00 2013 From: "sudipta sinha sudipta.mml__gmail.com" To: CCL Subject: CCL:G: neutralized system, solvent and pH effect in gaussian09 optimization Message-Id: <-49104-130823014313-30366-y0D4BI40JjXGfxSJOgfOcA,,server.ccl.net> X-Original-From: "sudipta sinha" Date: Fri, 23 Aug 2013 01:43:12 -0400 Sent to CCL by: "sudipta sinha" [sudipta.mml###gmail.com] Hi All, I want to optimize isopropylphosate using Gaussian 09 by considering the effect of solvent and pH. Moreover, isopropylphospahte has 2- charge and want to neutralize the system by adding some counter ions. What will the suitable approach to do that. I had tried with implicit solvent model by considering the keyword scrf=cpcm. It works well. But is there any better way to do that. Moreover, I tried to neutralize the system by adding one Mg2+ ion. However, I have a confusion regarding the placing of Mg2+ ion. Initially, I placed the ion at the close position of phosphate group. But the ion forms a bond after few iterations. Then I place the ion at a larger distance (4.0 A) and put a distance restraint between phosphorous and the ion. By this way the ion doesn't form a bond with phosphate group but I am not sure is it correct or not Finally, I am totally unaware how do I optimize a molecule at constant pH or pKa etc. Any suggestions, help will be highly appreciated. Best Sudipta From owner-chemistry@ccl.net Fri Aug 23 05:39:00 2013 From: "Adedapo Adeyinka u11335132.++.tuks.co.za" To: CCL Subject: CCL: Getting short contact data for molecule built with Gaussview Message-Id: <-49105-130823052558-12516-EytXSPUR1sxrNRH7lnl23Q++server.ccl.net> X-Original-From: Adedapo Adeyinka Content-Type: multipart/alternative; boundary=047d7b86e424080fad04e499fed0 Date: Fri, 23 Aug 2013 11:25:49 +0200 MIME-Version: 1.0 Sent to CCL by: Adedapo Adeyinka [u11335132-,-tuks.co.za] --047d7b86e424080fad04e499fed0 Content-Type: text/plain; charset=US-ASCII Dear All, I want to determine the distances of all the short contacts in a molecule I built with Gaussview and saved as a mol2 file. Does anyone know how to get this information automatically using gaussview or mercury? or is there any software that I can get for free to extract this data for me. I will be glad if anyone can help me out. Thanks Adedapo. -- This message and attachments are subject to a disclaimer. Please refer to http://www.it.up.ac.za/documentation/governance/disclaimer/ for full details. --047d7b86e424080fad04e499fed0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear All,
=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0I want to det= ermine the distances of all the short contacts in a molecule I built with G= aussview and saved as a mol2 file. Does anyone know how to get this informa= tion automatically using gaussview or mercury? =A0or is there any software = that I can get for free to extract this data for me.
I will be glad if anyone can help me out.


Thanks

Adedapo.

This message and attachments are subject to= a disclaimer. Please refer to=20 http://www.it.u= p.ac.za/documentation/governance/disclaimer/ for full details. --047d7b86e424080fad04e499fed0--