From owner-chemistry@ccl.net Sun Jul 29 01:05:00 2007
From: "Hoa Nguyen hoagiaonguyen%yahoo.com" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL: Program to fit the Fourier Series
Message-Id: <-34817-070729010349-30350-KdzIrYpOt9ShTJchp6vsRw]_[server.ccl.net>
X-Original-From: Hoa Nguyen <hoagiaonguyen^yahoo.com>
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Sent to CCL by: Hoa Nguyen [hoagiaonguyen]=[yahoo.com]
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Hi Loan,
   
  Give Matlab a try. It has a Curve Fitting toolbox. The command is "cftool".
   
  Good luck,
   
  Hoa Nguyen
  Department of Chemistry
  University of Utah

"Loan Huynh huynhkl2000(a)yahoo.ca" <owner-chemistry-$-ccl.net> wrote:
    Hi all,
   
  Does anyone know any program that can be used to fit the Fourier series into know values?  Any recommendation is greatly aprreciated!
   
  Fourier Transform:
  Vrb(fijkl) = V0 + 1/2(V1(1 + cos(y)) + V2(1 − cos(2y)) + V3(1 + cos(3y)))
  
Many thanks,
  Loan



       
---------------------------------
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<div>Hi Loan,</div>  <div>&nbsp;</div>  <div>Give Matlab a try. It has a Curve Fitting toolbox. The command is "cftool".</div>  <div>&nbsp;</div>  <div>Good luck,</div>  <div>&nbsp;</div>  <div>Hoa Nguyen</div>  <div>Department of Chemistry</div>  <div>University of Utah<BR><BR><B><I>"Loan Huynh huynhkl2000(a)yahoo.ca" &lt;owner-chemistry-$-ccl.net&gt;</I></B> wrote:</div>  <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">  <DIV><FONT face=courier>Hi all,</FONT></DIV>  <DIV><FONT face=courier></FONT>&nbsp;</DIV>  <DIV><FONT face=courier>Does anyone know any program that can be used to fit the Fourier series into&nbsp;know values?&nbsp; </FONT><FONT face=courier>Any recommendation is greatly aprreciated!</FONT></DIV>  <DIV><FONT face=courier></FONT>&nbsp;</DIV>  <DIV><FONT face=Courier>Fourier Transform:</FONT></DIV><FONT face=CMMI10>  <DIV align=left>V</FONT><FONT face=CMMI8>rb</FONT><FONT face=CMR10>(<SPAN style="FONT-SIZE:
 12pt; FONT-FAMILY: Symbol; mso-ascii-font-family: 'Times New Roman'; mso-fareast-font-family: 'Times New Roman'; mso-hansi-font-family: 'Times New Roman'; mso-bidi-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA; mso-char-type: symbol; mso-symbol-font-family: Symbol"><SPAN style="mso-char-type: symbol; mso-symbol-font-family: Symbol">f</SPAN></SPAN><FONT face=CMMI8 size=1>ijkl</FONT></FONT><FONT face=CMR10>) = </FONT><FONT face=CMMI10>V</FONT><FONT face=CMR8>0 </FONT><FONT face=CMR10>+ 1/2(</FONT><FONT face=CMMI10>V</FONT><FONT face=CMR8>1</FONT><FONT face=CMR10>(1 + cos(<SPAN style="FONT-SIZE: 12pt; FONT-FAMILY: Symbol; mso-ascii-font-family: 'Times New Roman'; mso-fareast-font-family: 'Times New Roman'; mso-hansi-font-family: 'Times New Roman'; mso-bidi-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA; mso-char-type: symbol;
 mso-symbol-font-family: Symbol"><SPAN style="mso-char-type: symbol; mso-symbol-font-family: Symbol">y</SPAN></SPAN></FONT><FONT face=CMR10>)) + </FONT><FONT face=CMMI10>V</FONT><FONT face=CMR8>2</FONT><FONT face=CMR10>(1 </FONT><FONT face=CMSY10>− </FONT><FONT face=CMR10>cos(2<SPAN style="FONT-SIZE: 12pt; FONT-FAMILY: Symbol; mso-ascii-font-family: 'Times New Roman'; mso-fareast-font-family: 'Times New Roman'; mso-hansi-font-family: 'Times New Roman'; mso-bidi-font-family: 'Times New   Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA; mso-char-type: symbol; mso-symbol-font-family: Symbol"><SPAN style="mso-char-type: symbol; mso-symbol-font-family: Symbol">y</SPAN></SPAN></FONT><FONT face=CMR10>)) + </FONT><FONT face=CMMI10>V</FONT><FONT face=CMR8>3</FONT><FONT face=CMR10>(1 + cos(3<SPAN style="FONT-SIZE: 12pt; FONT-FAMILY: Symbol; mso-ascii-font-family: 'Times New Roman'; mso-fareast-font-family: 'Times New Roman';
 mso-hansi-font-family: 'Times New Roman'; mso-bidi-font-family: 'Times New Roman'; mso-ansi-language: EN-US; mso-fareast-language: EN-US; mso-bidi-language: AR-SA; mso-char-type: symbol; mso-symbol-font-family: Symbol"><SPAN style="mso-char-type: symbol; mso-symbol-font-family: Symbol">y</SPAN></SPAN></FONT><FONT face=CMR10>)))</DIV></FONT>  <DIV><BR><FONT face=courier>Many thanks,</FONT></DIV>  <DIV><FONT face=courier>Loan<BR></FONT></DIV></BLOCKQUOTE><BR><p>&#32;
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From owner-chemistry@ccl.net Sun Jul 29 08:48:00 2007
From: "Igor Filippov Contr igorf]~[helix.nih.gov" <owner-chemistry-,-server.ccl.net>
To: CCL
Subject: CCL: Program to fit the Fourier Series
Message-Id: <-34818-070729081934-2288-oh+j2luqOihc4rZXGB3P1Q-,-server.ccl.net>
X-Original-From: "Igor Filippov [Contr]" <igorf|helix.nih.gov>
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Sent to CCL by: "Igor Filippov [Contr]" [igorf\a/helix.nih.gov]
Wolfram Mathematica can certainly do that.
http://www.wolfram.com/


Igor

On Sat, 2007-07-28 at 15:41 -0400, Loan Huynh huynhkl2000(a)yahoo.ca
wrote:
> Hi all,
>  
> Does anyone know any program that can be used to fit the Fourier
> series into know values?  Any recommendation is greatly aprreciated!
>  
> Fourier Transform:
> Vrb(fijkl) = V0 + 1/2(V1(1 + cos(y)) + V2(1 − cos(2y)) + V3(1 +
> cos(3y)))
> 
> Many thanks,
> Loan
> 
-- 
Igor Filippov [Contr] <igorf..helix.nih.gov>


From owner-chemistry@ccl.net Sun Jul 29 09:23:00 2007
From: "Sina T reli sinatureli^^^gmail.com" <owner-chemistry!^!server.ccl.net>
To: CCL
Subject: CCL: Using ZINDO/S on B800
Message-Id: <-34819-070729054024-26984-WBnCRAAI42GG6Uw1PFXxAw!^!server.ccl.net>
X-Original-From: "Sina  T  reli" <sinatureli|-|gmail.com>
Date: Sun, 29 Jul 2007 05:40:20 -0400


Sent to CCL by: "Sina  T  reli" [sinatureli _ gmail.com]
I have a project about bacteriochlorophllys which at some stage require spectroscoping information about them. For this reason I was trying to familiarize my-self with ZINDO/S on some trial molecules. I tried some calculations with bacteriochlophyll 800 (having a maximum peak at 800nm). The paramteres were 5 unoccupied, 5 occupied orbitals and the default paramters for overlap weight factors (1.267 for single, 0,585 for pi bonds) as they have been stated as quite efficient for biomolecules. I got one peak all right at 793 but it wasnt the highest peak unfortunately... There were some higher peaks at around 560 nm. Why would that be? In the hyperchem tutorial it says that ZINDO/S calculations may detect bands at lower wavelengths that a spectrophotometer wouldn't be able to detect, or something like that. Is that the reaons why I see those bands or am I doing something wrong? By the way the chlorophyll is imported from a pdb file but I deleted all the other parts like caretenoids and the protein etc (telling you this because if I had the caretenoids in the calculation it would be expected to have bands at around 500 nm)

Thanks
sincerly


From owner-chemistry@ccl.net Sun Jul 29 09:58:01 2007
From: "maxim totrov max*|*molsoft.com" <owner-chemistry++server.ccl.net>
To: CCL
Subject: CCL: MMFF94 type for HN or HN2?
Message-Id: <-34820-070728173530-24285-96WeYYwiG8S+wmNZyZnczw++server.ccl.net>
X-Original-From: maxim totrov <max#molsoft.com>
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Date: Sat, 28 Jul 2007 13:34:57 -0700
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Sent to CCL by: maxim totrov [max-$-molsoft.com]

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Type 23 in MMFF94 is specifically assigned to (among other things)  
pyrrole H-N (HPYL). Therefore it seems appropriate for H attached to  
aromatic N. Type 28 is primarily for amides and like.

Max Totrov

> Hello,
>
> I noticed that there is a confusion on atomic type in molecule  
> CEWVIJ10 in the dative.mol2 file of the mmff94 validation suite.  
> The hydrogen attached on N should be considered as HNCC/HNCN(type  
> 28) type since the 5-ring is aromatic. However, the log file of the  
> validation suite listed a type of HN (type 23), same type is listed  
> from several commercial softwares. Could anyone give me a hint on  
> what I am missing here?
>
> Thanks,
>
> Jansen
>
>
>
> Take the Internet to Go: Yahoo!Go puts the Internet in your pocket:  
> mail, news, photos & more.


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<HTML><BODY style=3D"word-wrap: break-word; -khtml-nbsp-mode: space; =
-khtml-line-break: after-white-space; "><DIV><BR =
class=3D"khtml-block-placeholder"></DIV><DIV>Type 23 in MMFF94 is =
specifically assigned to (among other things) pyrrole H-N (HPYL). =
Therefore it seems appropriate for H attached to aromatic N. Type 28 is =
primarily for amides and like.</DIV><DIV><BR =
class=3D"khtml-block-placeholder"></DIV><DIV>Max Totrov</DIV><DIV>=A0<BR =
class=3D"Apple-interchange-newline"><BLOCKQUOTE =
type=3D"cite">Hello,<BR><BR>I noticed that there is a confusion on =
atomic type in molecule CEWVIJ10 in the dative.mol<SPAN =
style=3D"font-family: monospace;"><SPAN style=3D"text-decoration: =
underline;"></SPAN></SPAN>2 file of the mmff94 validation suite. The =
hydrogen attached on N should be considered as HNCC/HNCN(type 28) type =
since the 5-ring is aromatic. However, the log file of the validation =
suite listed a type of HN (type 23), same type is listed from several =
commercial softwares. Could anyone give me a hint on what I am missing =
here?<BR><BR>Thanks,<BR><BR>Jansen<BR><BR><BR><DIV>       <BR =
class=3D"khtml-block-placeholder"></DIV><HR size=3D"1">Take the Internet =
to Go: Yahoo!Go puts the <A =
href=3D"http://us.rd.yahoo.com/evt=3D48253/*http://mobile.yahoo.com/go?ref=
er=3D1GNXIC">Internet in your pocket:</A> mail, news, photos &amp; =
more.</BLOCKQUOTE></DIV><BR></BODY></HTML>=

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