From owner-chemistry@ccl.net Fri Oct 21 01:27:00 2016 From: "Norrby, Per-Ola Per-Ola.Norrby__astrazeneca.com" To: CCL Subject: CCL: IR chemiluminescence? Message-Id: <-52455-161021012451-6035-snUTr400/J6rMkt+IXXq+Q(-)server.ccl.net> X-Original-From: "Norrby, Per-Ola" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_HE1PR04MB2092FC8C8B3F0E1E7DDB69E0CAD40HE1PR04MB2092eurp_" Date: Fri, 21 Oct 2016 05:24:41 +0000 MIME-Version: 1.0 Sent to CCL by: "Norrby, Per-Ola" [Per-Ola.Norrby.:.astrazeneca.com] --_000_HE1PR04MB2092FC8C8B3F0E1E7DDB69E0CAD40HE1PR04MB2092eurp_ Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: base64 U29tZSBhZGRpdGlvbnMuIEkgY29uY3VyLCBhZGRpdGlvbmFsIGNhbGN1bGF0aW9ucyBhcmUgbmVl ZGVkLCBsaWtlIGZ1bGwgUU0gdHJhbnNpdGlvbiBwcm9iYWJpbGl0aWVzLiBJ4oCZbSBub3Qgc3Vy ZSBob3cgYWNjdXJhdGUgb3IgcmVsZXZhbnQgc3VjaCBjYWxjdWxhdGlvbnMgYXJlLiBJbiBtb3N0 IGV4cGVyaW1lbnRhbCBzZXR1cHMgKGV4Y2VwdCBoaWdoIHZhY3V1bSkgdGhlIGVuZXJneSB3b3Vs ZCBiZSBkaXNzaXBhdGVkIGJ5IGNvbGxpc2lvbnMuIFRoZSBxdWVzdGlvbiBkb2VzIGNvbWUgdXAg aW4gaW50ZXJzdGVsbGFyIGNoZW1pc3RyeSwgeW91IGNvdWxkIHRyeSBsb29raW5nIGluIHRoYXQg 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Content-Type: multipart/alternative; boundary=001a114491ece75bd7053f599e69 Date: Fri, 21 Oct 2016 11:20:33 +0530 MIME-Version: 1.0 Sent to CCL by: Jeya Vimalan [jeyavimalan2k%%gmail.com] --001a114491ece75bd7053f599e69 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Dear All, Thanks for your response. I am summarizing the replies. vimal Question : =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Dear All, I have three composition. A1-B3-C4 A2-B4-C5 A4-B3-C7 I would like to understand which structures are stable and hence decided to calculate formation (or Cohesive) energy. Lets take the first two cases and calculate Formation energy by the below formulae. Formation Energy of 1 (E1) =3D Total energy of A1-B3-C4 -(Energy of 1*A + Energy of 3*B + Energy of 4*C). Formation Energy of 1 (E2) =3D Total energy of A2-B4-C5 -(Energy of 2*A + Energy of 4*B + Energy of 5*C). Does the direct comparison (E1, E2) makes sense? Can i conclude if E1>E2, then composition 1 is more stable. I feel, i am missing something. Your help would be appreciable. Best regards, Vimal =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D =3D=3D=3D Dear Vimal, I would say that your approach is valid, under the condition that the A, B, and C and sensible moieties. It reminds a bit of atomization energies. However, I would say that if E1 > E2 (e.g. +2 vs. -10) that 2 is more stable, not 1. Marce Prof Dr Marcel Swart, FRSC ICREA Research Professor at Institut de Qu=C3=ADmica Computacional i Cat=C3=A0lisi (IQCC) Univ. Girona (Spain) COST Action CM1305 (ECOSTBio) chair Girona Seminar 2016 organizer IQCC director Young Academy of Europe (Board) member Web http://www.marcelswart.eu vCard addressbook://www.marcelswart.eu/MSwart.vcf =3D=3D=3D=3Dl Dear Vimal: Unfortunately, the concept of stability is not that straightforward. Thermodynamics does not provide the final answer. The stability of a molecule not only depends on its formation energy, but it depends also on the relative energies of its neighboring local minima on its potential energy surface and the energy barrier between the minimum and its immediate neighboring minima (kinetic stability). To begin, I would rather check the depth of minimum energy well by looking at frequencies. In the next step ab initio/MC/DFT- MD simulations can provide more insight toward the kinetic stability. Then of course we can define stability with respect to a particular reaction. Is your molecule stable when it is in the presence of air/water/light/etc. You must be more precise about stability. I hope my general answer can help you to solve your problem. Good luck, Cina -------------------------------------------------------------- Cina Foroutan-Nejad, PhD CEITEC-Central European Institute of Technology Kamenice 5/A4, Masaryk University, Brno, Czech Republic https://muni.academia.edu/CinaForoutanNejad =3D=3D=3D=3D Hi Vimal: I am not exactly certain what you want to do but if you want to estimate is composition A1-B3-C4 is more stable than A2-B4-C5, you should calculate the energy of this "reaction" ... A1-B3-C4 + A + B + C --> A2-B4-C5 Now you have a mass balanced equation. Assuming the energies of these components are negative, then if E(Right Hand Side) - E(Left Hand Side) is negative the LHS is more stable. This means A2-B4-C5 as a compound is more stable than A1-B3-C4 and an extra A, B, and C. Regards, Joe Golab jtgolab59(~)gmail.com =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Dear Jeya, how are you? The comparison kind of makes sense, but to get the correct energies it is not enough to calculate the single points without the thermodynamic corrections (and using the correct stoichiometry in your equations). Please, if you can, take a look at this link[1] (it is in Portuguese, but maybe Google Translator can deal with this issue for you). All the best [1] - http://ab.cheminformatics.xyz/dft/uma-busca-pela-entalpia-de-formacao= / henriquecsj(~)gmail.com =3D=3D=3D Thanks and best regards, vimal --001a114491ece75bd7053f599e69 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Dear All,

Thanks for your response.
I am summarizing the replies.
vimal

Question :


=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
Dear = All,

I have three composition.

A1-B3-C4
A2-B4= -C5
A4-B3-C7

= I would like to understand
which structures are stable a= nd hence
decided to calculate formation (or Cohesive) en= ergy.

Lets take the first two ca= ses and=C2=A0
calculate Formation energy by the below fo= rmulae.


= Formation Energy of 1 (E1) =3D Total energy of A1-B3-C4 -(Energy of 1*A + E= nergy of 3*B + Energy of 4*C).
Formation Energy of 1 (E2= ) =3D Total energy of A2-B4-C5 -(Energy of 2*A + Energy of 4*B + Energy of = 5*C).


Do= es the direct comparison (E1, E2) makes sense?
Can i con= clude if E1>E2, then composition 1 is more stable.
I feel, i am missing something.
Yo= ur help would be appreciable.

Be= st regards,
Vimal
=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D
=3D=3D=3D
Dear Vimal,

I would say that your approach is valid, u= nder the condition that the A, B, and C and
sensible moieties. It reminds a bit of atomization energies.

Howe= ver, I would say that if E1 > E2 (e.g. =C2=A0+2 =C2=A0vs. -10) that 2 is= more stable, not 1.

Marce

Prof Dr Marcel Swart, FRSC
ICREA Research Professor at
Institut de Qu=C3=ADmica Computacional= i Cat=C3=A0lisi (IQCC)
Univ. Girona (Spain)

COST Action CM1305 (= ECOSTBio) chair
Girona Seminar 2016 organizer
IQCC director
Young = Academy of Europe (Board) member

=3D=3D=3D=3Dl


Dear Vim= al:

Unfortunately, the concept of = stability is not that straightforward. Thermodynamics does not provide the = final answer. The stability of a molecule not only depends on its formation= energy, but it depends also on the relative energies of its neighboring lo= cal minima on its potential energy surface and the energy barrier between t= he minimum and its immediate neighboring minima (kinetic stability). To beg= in, I would rather check the depth of minimum energy well by looking at fre= quencies. In the next step ab initio/MC/DFT- MD simulations can provide mor= e insight toward the kinetic stability. Then of course we can define stabil= ity with respect to a particular reaction. Is your molecule stable when it = is in the presence of air/water/light/etc.
You must be more precise about stability.=C2= =A0

I hope my general answer can h= elp you to solve your problem.

Good lu= ck,
Cina

--------------------------------------------------------= ------
Cina Foro= utan-Nejad, PhD
CEITEC-Central European Institute of Technology
Kamenice 5/A4, Masaryk University, Br= no, Czech Republic

=3D=3D=3D=3D
Hi Vimal:

I am not exactly certain what you wan= t to do but if you want to estimate is composition A1-B3-C4 is more stable = than A2-B4-C5, you should calculate the energy of this "reaction"= ...

A1-B3-C4 + A + B + C --> A2-B4= -C5

Now you have a mass balanced equat= ion. Assuming the energies of these components are negative, then if E(Righ= t Hand Side) - E(Left Hand Side) is negative=C2=A0the LHS is more stable. T= his means=C2=A0A2-B4-C5 as a compound is more stable than=C2=A0A1-B3-C4 and= an extra A, B, and C.

Regards,
Joe Golab
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D

Dear Jeya, how a= re you?
The comparison kind of makes = sense, but to get the correct energies it is not enough to calculate the si= ngle points without the thermodynamic corrections (and using the correct st= oichiometry in your equations).
Please, if you= can, take a look at this link[1] (it is in Portuguese, but maybe Google Tr= anslator can deal with this issue for you).
All the best
<= br>
[1] -=C2=A0http:= //ab.cheminformatics.xyz/dft/uma-busca-pela-entalpia-de-formacao/=
henriquecsj(~)gmail.com
=3D=3D=3D


Thanks= and best regards,
vimal
--001a114491ece75bd7053f599e69-- From owner-chemistry@ccl.net Fri Oct 21 07:58:01 2016 From: "Andreas Klamt klamt]|[cosmologic.de" To: CCL Subject: CCL: Free program/software for calculating logD? Message-Id: <-52457-161021014407-11578-8ixYmOFHuwImBMQHhL3Qng- -server.ccl.net> X-Original-From: Andreas Klamt Content-Type: multipart/alternative; boundary="------------2FEE91EF4EBA691414549EAB" Date: Fri, 21 Oct 2016 07:43:54 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt=-=cosmologic.de] This is a multi-part message in MIME format. --------------2FEE91EF4EBA691414549EAB Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit The calculation of logD should always be a two step procedure, consisting of the calculation of all species of the compound of interest (let us call it X) in water and in the organic phase (usually wet n-octanol, but itmay be alkane, or whatever) and the calculation of the partition coefficient of the neutral species. Usually the compound will be in a neutral form in the organic phase. Let usconsider this form as the reference form of X. Now you can calculate the partition coefficient P or logP with various approaches. For this part often group contribution methods as CLOGP or logKow (from EPA) will do a good job, as long as you stay in their range of validity, i.e. standard organic chemistry. But for logD you need in addition the portion of the compound X which is in this reference state in water. In water it can protonated, deprotonated, zwitterionic, tautomeric, .... Usually protonation and deprotonation is most important (but the other cases can happen as well). For the portion of protonated and deprotonated species you need to define the pH of water, usually set to 7.4. Then you need the pKa and pKb of the compound and use the Hendersson-Hasselbalch equation in order to get the portion of the different species. Now youcan correct the neutral partition coefficient by the speciation equilibrium. In other words: You have to calculate the free energy of all possible species of X in water (neutral, maybe multiple protonated, multiple deprotonated, zwitterion and tautomeric) at pH=7.4, build the partition function Z relative to the energy of the reference state, and calculate D = P*Z. Perhaps read the articles on the blind prediction challenge SAMPL5 on the logD(cyclohexane/water), which have just appeared as a special issue of JCAMD. (Un)fortunately the bet method in that contest is not free. It is our COSMOtherm program. Again, for standard organic chemistry you will find free software doing the job. But if you have some more complicated compounds (as those 53 drugs), you need a method which takes into account all possible complications. Best regards Andreas Am 21.10.2016 um 01:27 schrieb Yingduo Gao yingduo * yahoo.com: > Hi, > > A medicinal chemistry friend in academia is looking for a free > program/software to calculate logD? Any info or suggestion will be > really appreciated. > > Thanks, > > Ying -- -------------------------------------------------- Prof. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH & Co. KG Imbacher Weg 46 D-51379 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt^cosmologic.de web www.cosmologic.de [University address: Inst. of Physical and Theoretical Chemistry, University of Regensburg] HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt --------------2FEE91EF4EBA691414549EAB Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit
The calculation of logD should always be a two step procedure, consisting of the calculation of all species of the compound of interest (let us call it X) in water and in the organic phase (usually wet n-octanol, but itmay be alkane, or whatever) and the calculation of the partition coefficient of the neutral species.

Usually the compound will be in a neutral form in the organic phase. Let usconsider this form as the reference form of X. Now you can calculate the partition coefficient P or logP with various approaches. For this part often group contribution methods as CLOGP or logKow (from EPA) will do a good job, as long as you stay in their range of validity, i.e. standard organic chemistry.

But for logD you need in addition the portion of the compound X which is in this reference state in water. In water it can protonated, deprotonated, zwitterionic, tautomeric, ....
Usually protonation and deprotonation is most important (but the other cases can happen as well). For the portion of protonated and deprotonated species you need to define the pH of water, usually set to 7.4.
Then you need the pKa and pKb of the compound and use the Hendersson-Hasselbalch equation in order to get the portion of the different species. Now youcan correct the neutral partition coefficient by the speciation equilibrium. In other words: You have to calculate the free energy of all possible species of X in water (neutral, maybe multiple protonated, multiple deprotonated, zwitterion and tautomeric) at pH=7.4, build the partition function Z relative to the energy of the reference state, and calculate D = P*Z.

Perhaps read the articles on the blind prediction challenge SAMPL5 on the logD(cyclohexane/water), which have just appeared as a special issue of JCAMD. (Un)fortunately the bet method in that contest is not free. It is our COSMOtherm program.

Again, for standard organic chemistry you will find free software doing the job. But if you have some more complicated compounds (as those 53 drugs), you need a method which takes into account all possible complications.

Best regards

Andreas






Am 21.10.2016 um 01:27 schrieb Yingduo Gao yingduo * yahoo.com:
Hi, 

A medicinal chemistry friend in academia is looking for a free program/software to calculate logD? Any info or suggestion will be really appreciated.
 
Thanks,
 
Ying


-- 
--------------------------------------------------

Prof. Dr. Andreas Klamt
CEO / Geschäftsführer
COSMOlogic GmbH & Co. KG
Imbacher Weg 46
D-51379 Leverkusen, Germany

phone  	+49-2171-731681
fax    	+49-2171-731689
e-mail 	klamt^cosmologic.de
web    	www.cosmologic.de

[University address:      Inst. of Physical and
Theoretical Chemistry, University of Regensburg]

HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
--------------2FEE91EF4EBA691414549EAB-- From owner-chemistry@ccl.net Fri Oct 21 08:33:01 2016 From: "Andreas Klamt klamt.:.cosmologic.de" To: CCL Subject: CCL: Free program/software for calculating logD? Message-Id: <-52458-161021015241-3522-RQzbOLt1C+0ZJrLbWAh0Ew||server.ccl.net> X-Original-From: Andreas Klamt Content-Type: multipart/alternative; boundary="------------7B64BAD83EA9EADA07348448" Date: Fri, 21 Oct 2016 07:52:28 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt[-]cosmologic.de] This is a multi-part message in MIME format. --------------7B64BAD83EA9EADA07348448 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit Corrected version: The calculation of logD should always be a two step procedure, consisting of the calculation of all species of the compound of interest (let us call it X) in water and in the organic phase (usually wet n-octanol, but it may be alkane, or whatever) and the calculation of the partition coefficient of the neutral species. Usually the compound will be in a neutral form in the organic phase. Let usconsider this form as the reference form of X. Now you can calculate the partition coefficient P or logP with various approaches. For this part often group contribution methods as CLOGP or logKow (from EPA) will do a good job, as long as you stay in their range of validity, i.e. standard organic chemistry without tautomerisation. But for logD you need in addition the portion of the compound X which is in this reference state in water. In water it can protonated, deprotonated, zwitterionic, tautomeric, .... Usually protonation and deprotonation is most important (but the other cases can happen as well). For the portion of protonated and deprotonated species you need to define the pH of water, usually set to 7.4. Then you need the pKa and pKb of the compound and use the Hendersson-Hasselbalch equation in order to get the portion of the different species. Now youcan correct the neutral partition coefficient by the speciation equilibrium. In other words: You have to calculate the free energy of all possible species of X in water (neutral, maybe multiple protonated, multiple deprotonated, zwitterion and tautomeric) at pH=7.4, build the partition function Z relative to the energy of the reference state, and calculate D = P/Z. Perhaps read the articles on the blind prediction challenge SAMPL5 on the logD(cyclohexane/water), which have just appeared as a special issue of JCAMD. (Un)fortunately the bet method in that contest is not free. It is our COSMOtherm program. Again, for standard organic chemistry you will find free software doing the job. But if you have some more complicated compounds (as those 53 drugs), you need a method which takes into account all possible complications. Best regards Andreas Am 21.10.2016 um 01:27 schrieb Yingduo Gao yingduo * yahoo.com: > Hi, > > A medicinal chemistry friend in academia is looking for a free > program/software to calculate logD? Any info or suggestion will be > really appreciated. > > Thanks, > > Ying -- -------------------------------------------------- Prof. Dr. Andreas Klamt CEO / Geschäftsführer COSMOlogic GmbH & Co. KG Imbacher Weg 46 D-51379 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt[#]cosmologic.de web www.cosmologic.de [University address: Inst. of Physical and Theoretical Chemistry, University of Regensburg] HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt --------------7B64BAD83EA9EADA07348448 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: 8bit
Corrected version:

The calculation of logD should always be a two step procedure, consisting of the calculation of all species of the compound of interest (let us call it X) in water and in the organic phase (usually wet n-octanol, but it may be alkane, or whatever) and the calculation of the partition coefficient of the neutral species.

Usually the compound will be in a neutral form in the organic phase. Let usconsider this form as the reference form of X. Now you can calculate the partition coefficient P or logP with various approaches. For this part often group contribution methods as CLOGP or logKow (from EPA) will do a good job, as long as you stay in their range of validity, i.e. standard organic chemistry without tautomerisation.

But for logD you need in addition the portion of the compound X which is in this reference state in water. In water it can protonated, deprotonated, zwitterionic, tautomeric, ....
Usually protonation and deprotonation is most important (but the other cases can happen as well). For the portion of protonated and deprotonated species you need to define the pH of water, usually set to 7.4.
Then you need the pKa and pKb of the compound and use the Hendersson-Hasselbalch equation in order to get the portion of the different species. Now youcan correct the neutral partition coefficient by the speciation equilibrium. In other words: You have to calculate the free energy of all possible species of X in water (neutral, maybe multiple protonated, multiple deprotonated, zwitterion and tautomeric) at pH=7.4, build the partition function Z relative to the energy of the reference state, and calculate D = P/Z.

Perhaps read the articles on the blind prediction challenge SAMPL5 on the logD(cyclohexane/water), which have just appeared as a special issue of JCAMD. (Un)fortunately the bet method in that contest is not free. It is our COSMOtherm program.

Again, for standard organic chemistry you will find free software doing the job. But if you have some more complicated compounds (as those 53 drugs), you need a method which takes into account all possible complications.

Best regards

Andreas






Am 21.10.2016 um 01:27 schrieb Yingduo Gao yingduo * yahoo.com:
Hi, 

A medicinal chemistry friend in academia is looking for a free program/software to calculate logD? Any info or suggestion will be really appreciated.
 
Thanks,
 
Ying


-- 
--------------------------------------------------

Prof. Dr. Andreas Klamt
CEO / Geschäftsführer
COSMOlogic GmbH & Co. KG
Imbacher Weg 46
D-51379 Leverkusen, Germany

phone  	+49-2171-731681
fax    	+49-2171-731689
e-mail 	klamt[#]cosmologic.de
web    	www.cosmologic.de

[University address:      Inst. of Physical and
Theoretical Chemistry, University of Regensburg]

HRA 20653 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
Komplementaer: COSMOlogic Verwaltungs GmbH
HRB 49501 Amtsgericht Koeln, GF: Prof. Dr. Andreas Klamt
--------------7B64BAD83EA9EADA07348448-- From owner-chemistry@ccl.net Fri Oct 21 09:08:01 2016 From: "=?UTF-8?B?6JWt5q+F?= hsiaoyi0504- -gmail.com" To: CCL Subject: CCL: Free program/software for calculating logD? Message-Id: <-52459-161021021155-20615-6/7qxkI3ot/4ewUMsPdGnw=server.ccl.net> X-Original-From: =?UTF-8?B?6JWt5q+F?= Content-Type: multipart/alternative; boundary=001a113d5334df5454053f59eaa6 Date: Fri, 21 Oct 2016 06:11:38 +0000 MIME-Version: 1.0 Sent to CCL by: =?UTF-8?B?6JWt5q+F?= [hsiaoyi0504,gmail.com] --001a113d5334df5454053f59eaa6 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hello: Maybe ALOGPS:http://www.vcclab.org/lab/alogps/ CDK:http://cdk.sourceforge.net/ PaDEL:http://www.yapcwsoft.com/dd/padeldescriptor/ works for that. Thank You Yi Hsiao rjensen-#-ualberta.ca =E6=96=BC 2016=E5=B9=B410= =E6=9C=8821=E6=97=A5 =E9=80=B1=E4=BA=94 =E4=B8=8B=E5=8D=881:05=E5=AF=AB=E9= =81=93=EF=BC=9A Sent to CCL by: rjensen^ualberta.ca Have your friend contact me. I am not sure what you mean by 'calculate logD'. I know what logD is, but now what you want to calculate. Thanks, Dr. Roy Jensen (=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D)-----------------------------------------= =C2=A4 Lecturer, Chemistry W5-19, University of Alberta 780.248.1808 On Thu, 20 Oct 2016 23:27:09 +0000 (UTC), you wrote: >Hi, >A medicinal chemistry friend in academia is looking for a freeprogram/software to calculate logD? Any info or suggestion will be really appreciated. > > Thanks, > > Ying -=3D This is automatically added to each message by the mailing script =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--001a113d5334df5454053f59eaa6 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hello:

Maybe

ALOGPS:h= ttp://www.vcclab.org/lab/alogps/
CDK:http://cdk.sourceforge.= net/
PaDEL:http://www.yapcwsoft.com/dd/padeldescriptor/=

works for= that.

Tha= nk You

Yi = Hsiao

rjen= sen-#-= ualberta.ca <owner-chemistry.=.ccl.net> =E6=96=BC 2016=E5= =B9=B410=E6=9C=8821=E6=97=A5 =E9=80=B1=E4=BA=94 =E4=B8=8B=E5=8D=881:05=E5= =AF=AB=E9=81=93=EF=BC=9A

Sent to CCL by: rjensen^ualberta.ca
Have your friend contact me. I am not sure what you mean by 'calculate<= br class=3D"gmail_msg"> logD'. I know what logD is, but now what you want to calculate.

Thanks,
=C2=A0Dr. Roy Jensen
(=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D)-----------------------------------------= =C2=A4
=C2=A0Lecturer, Chemistry
=C2=A0W5-19, University of Alberta
=C2=A0780.248.1808



On Thu, 20 Oct 2016 23:27:09 +0000 (UTC), you wrote:

>Hi,=C2=A0
>A medicinal chemistry friend in academia is looking for=C2=A0a freeprog= ram/software to calculate logD? Any info or suggestion will be really appre= ciated.
>
>=C2=A0Thanks,
>
>=C2=A0Ying



-=3D This is automatically added to each message by the mailing script =3D-=

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--001a113d5334df5454053f59eaa6-- From owner-chemistry@ccl.net Fri Oct 21 09:43:01 2016 From: "Wei Li liwei0099^_^gmail.com" To: CCL Subject: CCL: calculate IR using Fourier transform of the velocity/dipole moment ACF Message-Id: <-52460-161021073451-13851-MzPk3z0OIHCwaERTS/Lbxg#%#server.ccl.net> X-Original-From: Wei Li Content-Type: multipart/alternative; boundary=94eb2c076a62d3ed5b053f5e6dac Date: Fri, 21 Oct 2016 04:34:15 -0700 MIME-Version: 1.0 Sent to CCL by: Wei Li [liwei0099 : gmail.com] --94eb2c076a62d3ed5b053f5e6dac Content-Type: text/plain; charset=UTF-8 Hi Friends, I want to calculate the IR of a complex from the given classical md trajectory, in xyz format. As known this can be achieved via the Fourier transform of the velocity/dipole moment autocorrelation function. Is there a program can do this? Any comments regarding the implement are greatly appreciated. Thanks -- *Wei Li* PhD student State Key Lab of Theoretical & Computational Chemistry Institute of Theoretical Chemistry Jilin University Changchun, 130023 P.R. China Email: liwei0099]_[gmail.com --94eb2c076a62d3ed5b053f5e6dac Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Hi Friends,

I want to calculate th= e IR of a complex from the given classical md=C2=A0trajectory, in xyz forma= t.
As known this can be achieved via the F= ourier=C2=A0t= ransform of the velocity/dipole moment autocorrelation function.

Is there a program can d= o this? Any comments regarding the implement are greatly appreciated.

Thanks
=


--
Wei Li
PhD student
State Key Lab of Theo= retical & Computational Chemistry
Institute of Theoretical Chemistry=
Jilin University
Changchun, 130023
P.R. China
--94eb2c076a62d3ed5b053f5e6dac-- From owner-chemistry@ccl.net Fri Oct 21 10:18:00 2016 From: "Laidig, Bill laidig.wd-#-pg.com" To: CCL Subject: CCL: Free program/software for calculating logD? Message-Id: <-52461-161021101222-6168-fMV1NfEcrooZpTS2KJuM4g++server.ccl.net> X-Original-From: "Laidig, Bill" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" Date: Fri, 21 Oct 2016 14:12:13 +0000 MIME-Version: 1.0 Sent to CCL by: "Laidig, Bill" [laidig.wd*o*pg.com] Try EpiSuite from Syracuse and the EPA: https://www.epa.gov/tsca-screening-tools/epi-suitetm-estimation-program-interface Bill