From owner-chemistry@ccl.net Sat Oct 13 08:36:00 2007 From: "chupvl chupvl~!~gmail.com" To: CCL Subject: CCL: (re-)relaxing molecules Message-Id: <-35377-071013082629-21724-XaFf6Z8WQoRk3hqJkLYt4w:server.ccl.net> X-Original-From: chupvl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Sat, 13 Oct 2007 15:26:35 +0400 MIME-Version: 1.0 Sent to CCL by: chupvl [chupvl|gmail.com] Hello! In my point there three main ways of 3D alignment of the molecules - point-2-point matching as in MATCH potion of Sybyl - pharmacophoric matching - receptor-based alignment (You'll be using MATCH option after docking of series of molecules) and one more (I don't met an article about this but I think it's exist - is molecular descriptors alignment after descriptors selection based eg on good QSAR model) Vladimir Chupakhin MSU, Dpt. of Chemistry, Moscow, Russia aps1968**googlemail.com wrote: > Sent to CCL by: aps1968*|*googlemail.com > Dear CClrs, > > in order to perform CoMFA computations in Sybyl, I aligned my already > externally optimized molecules with the use of the function MATCH, taking > into account the fragment common for all molecules. The referee of the paper > however asks if the molecules were re-relaxed after the MATCH procedure. > I am not quite sure I understand what he means. Should I again in the > new positions perform any further optimization? They are already > optimized. He also > suggests a pharmacofore based alignment prior to comfa and again asks to > consider relaxing the conformers after MATCH alignment prior to comfa. > Any comments to that? Which alternative alignment methods can be > recommended to a SYBYL user? > > Regards, > > Andy> > > > > From owner-chemistry@ccl.net Sat Oct 13 18:38:01 2007 From: "=?ISO-8859-1?Q?Sina_T=FCreli?= sinatureli|a|gmail.com" To: CCL Subject: CCL: Questions Regarding Orbitals/UV-Visible Absorption && CI Spaces Message-Id: <-35378-071013183446-12933-65pBEiFbJSsYeK1r+tLcjQ|,|server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Sina_T=FCreli?=" Content-Type: multipart/alternative; boundary="----=_Part_21336_26025334.1192314871318" Date: Sun, 14 Oct 2007 01:34:31 +0300 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Sina_T=FCreli?=" [sinatureli() gmail.com] ------=_Part_21336_26025334.1192314871318 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline You helped me thanks. Though I think that structure of chlorophyll molecules SHOULD be different in solution or atleast in vacuum, in terms of steric hinderences which contiributes to Qx. It is the protein scaffold and the ankorage between the tails of the chlorophylls that gives the chlorophyll ring a slightly more strained form. When optimized in vacuum Qx, as I expected, drops down to about 650 (which I assume is no more qx?). Although ofcourse vacuum would give a more different structure than that would have been in solution, but chlorophylls arent in solution in their local enviroment neither. And also doing semiempirical calculations with a chlorophyll in water molecules would be very time demanding. That is, if I do not grossly over estimate it by saying that it is a 1:1 solution and optimize a chlorophyll molecule with a water molecule as a ligand to its central MG atom. This ofcourse does not simulate the effect of the water on the hydrophobic parts of the chlorophyll and the ring which I assume is the main contributer to Qx along with interraction of N orbitals with conjugated pi orbitals. And also as you said, I am more interested in changes in spectra values rather than their exact values though your message and several other sources have been helpful for me to select a CI space (which I guess will be 10,10). And also have you any ideas on how to make logical connections between nitrogen orbital shapes, localizations with changes in spectra? As far as I know, such a high UV absorbance (around 800) needs to involve transtion from a N orbital to conjugated pi orbitals... Thanks a lot for your answers. On 10/11/07, Igor Avilov avilovi{}averell.umh.ac.be wrote: > > > Sent to CCL by: "Igor Avilov" [avilovi::averell.umh.ac.be] > Dear Sina, > > The 4-orbital model is often used to explain the trends in the spectra > of tetrapyrrolic compounds. It is based on the fact that in many cases 2 > HOMOs and 2 LUMOs are separated from the lower/higher energy orbitals by > the considerable energy gaps. Thus, one-electron excitation between > these 4 frontier MOs are likely to play a dominant role in the formation > of the lowest transitions in the absorption spectrum. But it does not > mean that the other one-electron excited configurations cannot mix with > them. This admixture is larger, of cause, for the B-states, as they have > higher energy than the Q-states. So one must use a sufficiently large > basis for CI calculations. On my personal experience, 10 HOMOs x 10 > LUMOs is enough for the calculation of the excited states of the > porphyrin monomers. If you will use minimal bases like 2 HOMOs x 2 LUMOs > (4-orbital model), you could get into trouble even if you are interested > only in the several lowest excited states. By the way, I suspect that in > this basis you would get the energies of the B-states completely wrong > (even if the energies of the Q-states seem to be good). Once I performed > such calculations (with 2 x 2 basis) and at the end I had to simply > throw away the results. > > The fact that semi-empirical methods like CNDO/S and INDO/S give the > energy of the Q-states lower than the experimental values, it's not a > big problem, on my opinion. What is important - is to get the trends > right, and here the semi-empirical methods do a very nice job. TD-DFT, > for example, also does not assure quantitative agreement with the > experiment (look at the paper of D. Sundholm "A > density-functional-theory study of bacteriochlorophyll b", PHYSICAL > CHEMISTRY CHEMICAL PHYSICS 5 (19): 4265-4271 OCT 1 2003). > > On my opinion you can use the structure from the pdb-file (containing > the experimental crystal structure of the molecule, I suppose), although > in solution your molecule may have slightly different geometry. The > results should not be dramatically different if you perform geometry > optimization first. Anyway, the most important thing is not to get > theoretical spectrum very-very close to the experimental one, which > could be (or even usually is) just due to the lucky cancellation of > errors. > > I hope I helped you a little bit... > > Igor Avilov. > > -----Original Message----- > > From: owner-chemistry(0)ccl.net [mailto:owner-chemistry(0)ccl.net] > Sent: jeudi 11 octobre 2007 12:40 > To: Igor Avilov > Subject: CCL: Questions Regarding Orbitals/UV-Visible Absorption && CI > Spaces > > > Sent to CCL by: "Sina T reli" [sina.tureli, boun.edu.tr] > > I have some questions regarding qualitative reasoning about how to > corralate orbital localizations with uv-visible absorption and also size > CI spaces to be used in detecting the bands of bacteriochlorophylls. > > 1. It is known that bacteriochlorophylls usually have qx bands around > 700-800nm. And that can be accounted to effect of both conjugation and > the jumping of electrons from nitrogen orbitals to the conjugated pi > orbitals of the system. How ever still knowing that I am not able to > qualitatively reason on how the orbitals localization and size effect > the osscilator strength and absorption. Given below are the orbitals > that contirbute to the Qx (830nm) of bacteriochlorophyll a. The > transition L->H is the dominant one. This calculation is performed on > the nonoptimized chlorophyll taken from a pdb with arguslab using (5,5) > CI space. The qx absorbance was seen to be about 833 nm. So in short, > why would the third transition be the one with the higher oscillator > strength or why would these orbitals specifically contirbute to 830nm > absorbance, how can be make qualitative reasoning about > orbital-absorbance relatedness. Any sources of study as an answer is > also welcome. > > http://img518.imageshack.us/img518/4318/qyyc5.jpg > > 2. In literature and in some discssions that Mark Thompson (creator of > the arguslab program) has participated in this list, it is said that a > CI space of (20,20) is optimal for such large molecules... But 20,20 > gives about 950 nm while 5,5 gives about 830 nm (which is very close). > And also according to the four orbital model (which can also be > visiualized by plotting the energies of the orbitals), 4,4 CI space > shuld be enough to visiualize the Qx reagion, shouldnt it be? Keep in > mind that I performed the calculations only the chlorophyll not the > whole complex. > > > 3. Finally, would performing CI calculations on a chlorophyll taken > directly from pdb give reliable results or would some kind of > optimization of the chlorophyll molecule required to get reliable > results? > > Thanks for your kind answers...http://www.ccl.net/spammers.txt > > > > - This is automatically added to each message by the mailing script -> > > > ------=_Part_21336_26025334.1192314871318 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline You helped me thanks. Though I think that structure of chlorophyll molecules SHOULD be different in solution or atleast in vacuum, in terms of steric hinderences which contiributes to Qx. It is the protein scaffold and the ankorage between the tails of the chlorophylls that gives the chlorophyll ring a slightly more strained form. When optimized in vacuum Qx, as I expected, drops down to about 650 (which I assume is no more qx?).

Although ofcourse vacuum would give a more different structure than that would have been in solution, but chlorophylls arent in solution in their local enviroment neither. And also doing semiempirical calculations with a chlorophyll in water molecules would be very time demanding. That is, if I do not grossly over estimate it by saying that it is a 1:1 solution and optimize a chlorophyll molecule with a water molecule as a ligand to its central MG atom. This ofcourse does not simulate the effect of the water on the hydrophobic parts of the chlorophyll and the ring which I assume is the main contributer to Qx along with interraction of N orbitals with conjugated pi orbitals.

 And also as you said, I am more interested in changes in spectra values rather than their exact values though your message and several other sources have been helpful for me to select a CI space (which I guess will be 10,10).

And also have you any ideas on how to make logical connections between nitrogen orbital shapes, localizations with changes in spectra? As far as I know, such a high UV absorbance (around 800) needs to involve transtion from a N orbital to conjugated pi orbitals...

Thanks a lot for your answers.

On 10/11/07, Igor Avilov avilovi{}averell.umh.ac.be < owner-chemistry _ ccl.net> wrote:

Sent to CCL by: "Igor Avilov" [avilovi::averell.umh.ac.be]
Dear Sina,

The 4-orbital model is often used to explain the trends in the spectra
of tetrapyrrolic compounds. It is based on the fact that in many cases 2
HOMOs and 2 LUMOs are separated from the lower/higher energy orbitals by
the considerable energy gaps. Thus, one-electron excitation between
these 4 frontier MOs are likely to play a dominant role in the formation
of the lowest transitions in the absorption spectrum. But it does not
mean that the other one-electron excited configurations cannot mix with
them. This admixture is larger, of cause, for the B-states, as they have
higher energy than the Q-states. So one must use a sufficiently large
basis for CI calculations. On my personal experience, 10 HOMOs x 10
LUMOs is enough for the calculation of the excited states of the
porphyrin monomers. If you will use minimal bases like 2 HOMOs x 2 LUMOs
(4-orbital model), you could get into trouble even if you are interested
only in the several lowest excited states. By the way, I suspect that in
this basis you would get the energies of the B-states completely wrong
(even if the energies of the Q-states seem to be good). Once I performed
such calculations (with 2 x 2 basis) and at the end I had to simply
throw away the results.

The fact that semi-empirical methods like CNDO/S and INDO/S give the
energy of the Q-states lower than the experimental values, it's not a
big problem, on my opinion. What is important - is to get the trends
right, and here the semi-empirical methods do a very nice job. TD-DFT,
for example, also does not assure quantitative agreement with the
experiment (look at the paper of D. Sundholm "A
density-functional-theory study of bacteriochlorophyll b", PHYSICAL
CHEMISTRY CHEMICAL PHYSICS 5 (19): 4265-4271 OCT 1 2003).

On my opinion you can use the structure from the pdb-file (containing
the experimental crystal structure of the molecule, I suppose), although
in solution your molecule may have slightly different geometry. The
results should not be dramatically different if you perform geometry
optimization first. Anyway, the most important thing is not to get
theoretical spectrum very-very close to the experimental one, which
could be (or even usually is) just due to the lucky cancellation of
errors.

I hope I helped you a little bit...

Igor Avilov.

-----Original Message-----
> From: owner-chemistry(0)ccl.net [mailto: owner-chemistry(0)ccl.net]
Sent: jeudi 11 octobre 2007 12:40
To: Igor Avilov
Subject: CCL: Questions Regarding Orbitals/UV-Visible Absorption && CI
Spaces


Sent to CCL by: "Sina  T  reli" [sina.tureli, boun.edu.tr]

I have some questions regarding qualitative reasoning about how to
corralate orbital localizations with uv-visible absorption and also size
CI spaces to be used in detecting the bands of bacteriochlorophylls.

1. It is known that bacteriochlorophylls usually have qx bands around
700-800nm. And that can be accounted to effect of both conjugation and
the jumping of electrons from nitrogen orbitals to the conjugated pi
orbitals of the system. How ever still knowing that I am not able to
qualitatively reason on how the orbitals localization and size effect
the osscilator strength and absorption. Given below are the orbitals
that contirbute to the Qx (830nm) of bacteriochlorophyll a. The
transition L->H is the dominant one. This calculation is performed on
the nonoptimized chlorophyll taken from a pdb with arguslab using (5,5)
CI space. The qx absorbance was seen to be about 833 nm. So in short,
why would the third transition be the one with the higher oscillator
strength or why would these orbitals specifically contirbute to 830nm
absorbance, how can be make qualitative reasoning about
orbital-absorbance relatedness. Any sources of study as an answer is
also welcome.

http://img518.imageshack.us/img518/4318/qyyc5.jpg

2. In literature and in some discssions that Mark Thompson (creator of
the arguslab program) has participated in this list, it is said that a
CI space of (20,20) is optimal for such large molecules... But 20,20
gives about 950 nm while 5,5 gives about 830 nm (which is very close).
And also according to the four orbital model (which can also be
visiualized by plotting the energies of the orbitals), 4,4 CI space
shuld be enough to visiualize the Qx reagion, shouldnt it be? Keep in
mind that I performed the calculations only the chlorophyll not the
whole complex.


3. Finally, would performing CI calculations on a chlorophyll taken
directly from pdb give reliable results or would some kind of
optimization of the chlorophyll molecule required to get reliable
results?

Thanks for your kind answers...


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