From owner-chemistry@ccl.net Fri Nov 4 04:58:12 2005 From: "Marc Baaden baaden;;smplinux.de" To: CCL Subject: CCL: Dipole moment calculation from non-zero charge distribution Message-Id: <-29875-051104045302-2851-rNRnCFiiyV7ZwWtS63fJ2Q * server.ccl.net> X-Original-From: "Marc Baaden" Sent to CCL by: "Marc Baaden" [baaden^^^smplinux.de] Dear CCL readers, I am looking for a formular/recipe to calculate the dipole moment for a charged molecule. In that case my guess is that you first have to "factor out"/remove the monopole, but I couldn't find a precise formula for this case. In one textbook the dipole moment is simply given as the integral over r*p(r) where r is the position of the charge and p(r) the charge density at r. But for a charge distribution with net charge, this does not correspond to a separation of equal amounts of positive and negative charge ... ... as a naive suggestion, I could imagine calculating the geometrical centre of all negative charge and of all positive charge, remove the monopole charge from those and then calculate the dipole moment for this. But I would like confirmation (maybe even a reference or textbook) that explicitly handles this case. Thanks in advance, Marc Baaden NB: maybe I should add that this is for a classic (molecular mechanics) model of a protein with fixed point charges. The protein is charged due to the protonation states of its ionizable residues. Also in this context, is there a software package that can take a charge distribution (ideally a PDB file with charges in the last column) and calculate monopole + dipole + octapole + hexadecapole moments for this ? -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden[]smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 From owner-chemistry@ccl.net Fri Nov 4 07:20:00 2005 From: "Orlin Blajiev blajiev^_^vub.ac.be" To: CCL Subject: CCL:G: transition moments Message-Id: <-29876-051104060740-25017-ix4VLvpLyATgj2EVq+H/uw#,#server.ccl.net> X-Original-From: "Orlin Blajiev" Sent to CCL by: "Orlin Blajiev" [blajiev~~vub.ac.be] Hi everybody, I will very appreciate if somebody lets me know how to get the direction of the vibrational transition dipole moments out of the Gaussian or Gamess output. They can be visualized by Gaussview, but I do not know how to relate them to the molecular coordination system. Thank you in advance. Orlin blajiev ~ vub ac be From owner-chemistry@ccl.net Fri Nov 4 07:54:01 2005 From: "Patrick Senet Patrick.Senet[a]u-bourgogne.fr" To: CCL Subject: CCL: Dipole moment calculation from non-zero charge distribution Message-Id: <-29877-051104073740-19041-wq4t3Fy4WEyGHqy+ML1qxg###server.ccl.net> X-Original-From: "Patrick Senet" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 4 Nov 2005 12:56:17 +0100 MIME-Version: 1.0 Sent to CCL by: "Patrick Senet" [Patrick.Senet(a)u-bourgogne.fr] Hi, In fact the dipole of a charged system depends on the choice of the origin of the coordinates. In other words, the dipole is not translation invariant. The formula to compute the dipole in your case with fixed charges is indeed simply P=sum(over all atoms K) Q(K) R(K) where Q(K) is the charge of atom K, R(K) its position. You can defined now a molecular dipole by adding and substracting any vector U: P=sum(over all atoms K) Q(K) (R(K)-U) + U sum(over all atoms K) Q(K), The first sum is invariant by translation of the molecule, the second depends on the net charge of the molecule. The choice of U is arbitrary ! A convenient choice in MD is the center of mass (or geometrical center), then you can define a molecular dipole as the first term. By setting the origin at the mass center the second term vanishes. Hope this help, Patrick Senet (We used this recently in "A DFT study of polarisabilities and dipole moments of water clusters", M. Yang, P. Senet and C. Van Alsenoy, Int. J. of Quant. Chem. 101 (2005), 535-542.) ----- Original Message ----- > From: "Marc Baaden baaden;;smplinux.de" To: "Senet, Patrick, Cnrs Umr 5027 " Sent: Friday, November 04, 2005 11:22 AM Subject: CCL: Dipole moment calculation from non-zero charge distribution > > Sent to CCL by: "Marc Baaden" [baaden^^^smplinux.de] > Dear CCL readers, > > I am looking for a formular/recipe to calculate the dipole moment > for a charged molecule. In that case my guess is that you first > have to "factor out"/remove the monopole, but I couldn't find a > precise formula for this case. > > In one textbook the dipole moment is simply given as the integral > over r*p(r) where r is the position of the charge and p(r) the charge > density at r. But for a charge distribution with net charge, this does not > correspond to a separation of equal amounts of positive and negative > charge ... > > .. as a naive suggestion, I could imagine calculating the geometrical > centre of all negative charge and of all positive charge, remove the > monopole charge from those and then calculate the dipole moment for this. > But I would like confirmation (maybe even a reference or textbook) that > explicitly handles this case. > > Thanks in advance, > Marc Baaden > > NB: maybe I should add that this is for a classic (molecular mechanics) > model of a protein with fixed point charges. The protein is charged > due to the protonation states of its ionizable residues. > > Also in this context, is there a software package that can take a > charge distribution (ideally a PDB file with charges in the last > column) and calculate monopole + dipole + octapole + hexadecapole > moments for this ? > -- > Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris > mailto:baaden _ smplinux.de - http://www.baaden.ibpc.fr > FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217> > From owner-chemistry@ccl.net Fri Nov 4 08:29:00 2005 From: "David F. Green dfgreen:+:ams.sunysb.edu" To: CCL Subject: CCL: Dipole moment calculation from non-zero charge distribution Message-Id: <-29878-051104072058-31034-Je68ZFlBuSTYPl7uu8GMdQ%x%server.ccl.net> X-Original-From: "David F. Green" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 04 Nov 2005 06:41:42 -0500 MIME-Version: 1.0 Sent to CCL by: "David F. Green" [dfgreen{=}ams.sunysb.edu] Marc, The standard definition of the dipole moment holds regardless of the net charge. However, the problem is that the dipole moment is translationally dependent; you will obtain a different dipole moment depending on what centre of expansion you choose. In general, only the leading term of any multipole expansion is invariant in this manner. If you are simply looking for a natural point of expansion, there are a view choices: 1. The centre of charge (this is the same as your suggestion). In this case, the dipole moment VANISHES, making the calculation pretty easy :) However, higher order terms will be non-zero and need to be calculated. An interesting pair of papers to read about this (and also how to define an analogous centre of dipole for neutral molecules) are: Platt, D. E. and Sliverman, B. D. J. Comput. Chem. 17:358-366 (1996). Silverman, B. D. and Platt, D. E. J. Med. Chem. 39:2129-2140 (1996) 2. The geometric centre of the molecule. There is no formal reason why this is a good choice, but it is a common one. Certainly, it is better to expand around a point within the boundary of the set of atoms. For a good example of why, thinking about what the dipole moment of a charged molecule would be if you expand around a point far away from the molecule. 3. If you are working with a set of related molecules, you may choose an expansion point defined by the common region. For example, choose the centre of the phenyl ring for a set of modified benzenes. If you are working a set of molecules with pre-defined positions and orientations (such as a set of bound ligand structures in a binding site) you may also use this information to define a common centre of expansion. I should point out though, that due to the translational variance problem, you should be very careful about what you use the multipole expansion for. The expansion is great for reducing the complexity of the system, and giving a few variables describing the majority of the electrostatic interactions. The choice of the centre of expansion may affect the convergence properties, so a reasonable choice is important. However, the individual values (with the exception of the leading term) are pretty much meaningless. Trying to read too much into the value of non-leading terms is a commonly made mistake; only the full expansion (all terms) up to some cutoff is relevant. I hope this helps. Cheers, David. ======================================================================== David F. Green Assistant Professor http://www.ams.sunysb.edu/~dfgreen/ Applied Mathematics and Statistics Stony Brook University Office: +1-631-632-9344 Math Tower, Room 1-117 Mobile: +1-617-953-3922 Stony Brook, NY 11794-3600 Fax: +1-631-632-8490 ======================================================================== Marc Baaden baaden;;smplinux.de wrote: > Sent to CCL by: "Marc Baaden" [baaden^^^smplinux.de] > Dear CCL readers, > > I am looking for a formular/recipe to calculate the dipole moment > for a charged molecule. In that case my guess is that you first > have to "factor out"/remove the monopole, but I couldn't find a > precise formula for this case. > > In one textbook the dipole moment is simply given as the integral > over r*p(r) where r is the position of the charge and p(r) the charge > density at r. But for a charge distribution with net charge, this does not > correspond to a separation of equal amounts of positive and negative > charge ... > > .. as a naive suggestion, I could imagine calculating the geometrical > centre of all negative charge and of all positive charge, remove the > monopole charge from those and then calculate the dipole moment for this. > But I would like confirmation (maybe even a reference or textbook) that > explicitly handles this case. > > Thanks in advance, > Marc Baaden > > NB: maybe I should add that this is for a classic (molecular mechanics) > model of a protein with fixed point charges. The protein is charged > due to the protonation states of its ionizable residues. > > Also in this context, is there a software package that can take a > charge distribution (ideally a PDB file with charges in the last > column) and calculate monopole + dipole + octapole + hexadecapole > moments for this ? From owner-chemistry@ccl.net Fri Nov 4 11:14:00 2005 From: "Marc Baaden baaden.__.smplinux.de" To: CCL Subject: CCL: Dipole moment calculation from non-zero charge distribution Message-Id: <-29879-051104105915-9637-N0KpUWeSoBXMULGKXj98qg__server.ccl.net> X-Original-From: Marc Baaden Content-Type: text/plain; charset=us-ascii Date: Fri, 04 Nov 2005 16:13:14 +0100 Mime-Version: 1.0 Sent to CCL by: Marc Baaden [baaden%a%smplinux.de] David, thank you for the very enlightening comments, suggestions and references. >>> "David F. Green dfgreen:+:ams.sunysb.edu" said: >> The standard definition of the dipole moment holds regardless of the net >> charge. [..] Hmm, I'd like to ask: what is the standard definition of a molecular dipole ? In several textbooks I found definitions along the line of "A dipole is a pair of electric charges of equal magnitude but opposite polarity [..]" which *implies* that the net charge is zero. This was also IMHO the "classical" and somewhat intuitive definition. I guess the second moment definition as integral over charge times position vector would be a better/more general definition. But what makes these definitions equivalent or allows to expand from one to the other ? (The first definition a priori breaking down for charged species) Also there must be a rationale to discard other definitions, eg one could dream up a definition of a molecular dipole as sum of all bond dipoles ? Are there seminal references on this ? Thanks, Marc Baaden -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden_-_smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 From owner-chemistry@ccl.net Fri Nov 4 11:48:00 2005 From: "Phil Hultin hultin.:.cc.umanitoba.ca" To: CCL Subject: CCL: Dipole Moments and Molecular Fragments Message-Id: <-29880-051104114208-26146-bCaPOzjGcSYG1m6pFbl7xg*_*server.ccl.net> X-Original-From: "Phil Hultin" Content-Type: multipart/alternative; boundary="----=_NextPart_000_000A_01C5E125.203F5C30" Date: Fri, 4 Nov 2005 09:49:53 -0600 MIME-Version: 1.0 Sent to CCL by: "Phil Hultin" [hultin|*|cc.umanitoba.ca] This is a multi-part message in MIME format. ------=_NextPart_000_000A_01C5E125.203F5C30 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit The question about dipole moments of charged species is related to another issue, which is somewhat of a hobby-horse of mine. In organic chemistry and biochemistry particularly, structural and mechanistic rationales are often based on the idea of "fragment dipoles" and their interactions with one another. In small molecules these are usually dipoles said to be associated with polar covalent bonds, while in proteins the so-called helix dipole is another example. For many years I accepted the idea that "intramolecular dipole-dipole repulsions" were good explanations for all kinds of phenomena, but I am in serious doubt about that idea now. When you start to dissect the overall dipole moment of a molecule, you enter into the same kind of origin-dependence that you see in ions. What makes the arbitrary choice of a bond dipole or a helix dipole more significant than the infinitude of other point-to-point dipoles that could be defined within the molecular charge envelope? I think chemists have attached too much significance to the undeniable separation of charge that exists between bonded atoms of different electronegativities, mainly because there was no way to demonstrate that these charge separations were not necessarily quantitatively or qualitatively different from any others that might be defined for the system. We have looked at charge distributions to seek evidence for fragment dipoles and their interactions, and we haven't seen anything convincing. Do others have any opinions on this? Dr. Philip G. Hultin Associate Professor of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 hultin%a%cc.umanitoba.ca http://umanitoba.ca/chemistry/people/hultin ------=_NextPart_000_000A_01C5E125.203F5C30 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

The question about dipole moments of charged species = is related to another issue, which is somewhat of a hobby-horse of = mine.

 

In organic chemistry and biochemistry particularly, structural and mechanistic rationales are often based on the idea of = “fragment dipoles” and their interactions with one another.  In small = molecules these are usually dipoles said to be associated with polar covalent = bonds, while in proteins the so-called helix dipole is another = example.

 

For many years I accepted the idea that = “intramolecular dipole-dipole repulsions” were good explanations for all kinds of phenomena, but I am in serious doubt about that idea now.  When you = start to dissect the overall dipole moment of a molecule, you enter into the same = kind of origin-dependence that you see in ions.  What makes the = arbitrary choice of a bond dipole or a helix dipole more significant than the infinitude of = other point-to-point dipoles that could be defined within the molecular charge envelope?  I think chemists have attached too much significance to = the undeniable separation of charge that exists between bonded atoms of = different electronegativities, mainly because there was no way to demonstrate that = these charge separations were not necessarily quantitatively or qualitatively different from any others that might be defined for the = system.

 

We have looked at charge distributions to seek = evidence for fragment dipoles and their interactions, and we haven’t seen = anything convincing.  Do others have any opinions on = this?

 

Dr. Philip G. Hultin

Associate Professor of = Chemistry,

University of Manitoba

Winnipeg, MB

R3T 2N2

hultin%a%cc.umanitoba.ca

http://umanitoba.ca/= chemistry/people/hultin

 

------=_NextPart_000_000A_01C5E125.203F5C30-- From owner-chemistry@ccl.net Fri Nov 4 12:41:01 2005 From: "Patrick Senet Patrick.Senet**u-bourgogne.fr" To: CCL Subject: CCL: Dipole moment calculation from non-zero charge distribution Message-Id: <-29881-051104121710-10518-N7CdpzYbA2BowA1QP3ZusQ[a]server.ccl.net> X-Original-From: "Patrick Senet" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 4 Nov 2005 18:17:05 +0100 MIME-Version: 1.0 Sent to CCL by: "Patrick Senet" [Patrick.Senet]=[u-bourgogne.fr] > I guess the second moment definition as integral over charge times position > vector would be a better/more general definition. But what makes > these definitions equivalent or allows to expand from one to the other ? > (The first definition a priori breaking down for charged species) > Dear Marc Baaden, Yes indeed, the most general definition of multipole moments came from the expansion of the electric potential of a charge density (confined in a sphere of large radius) in spherical harmonics. The dipole moment is defined by the integral of r*density in all cases. For two opposite point charges represented by Dirac Delta functions you recover the > pair of electric charges of equal magnitude but opposite polarity [..]" An electrostatic theorem tells you that the lowest nonvanishing multipole moment of any charge distribution is independent of the choice of the coordinates but all higher multipole moments are not in general translationaly invariant. In other words, a charged system has a dipole depending on the choice of coordinates. For two opposite charges, the monopole vanishes and the dipole is invariant. Best regards, Patrick Senet Prof. Patrick Senet Théorie de la matière condensée CNRS-UMR 5027, LPUB, Univ. de Bourgogne 9 Avenue Alain Savary - BP 47870 F-21078 Dijon Cedex Tel: 03 80 39 5922 Fax:03 80 39 6024 psenet(0)u-bourgogne.fr http://www;u-bourgogne.fr/LPUB From owner-chemistry@ccl.net Fri Nov 4 13:15:00 2005 From: "David F. Green dfgreen^mit.edu" To: CCL Subject: CCL: Dipole moment calculation from non-zero charge distribution Message-Id: <-29882-051104130226-5568-ECxn42pGfqdlUa2FI0igAg[]server.ccl.net> X-Original-From: "David F. Green" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 04 Nov 2005 12:24:44 -0500 MIME-Version: 1.0 Sent to CCL by: "David F. Green" [dfgreen_+_mit.edu] A dipole is just what you say, two equal and opposite charges; the dipole MOMENT is the second term in the multipole expansion. A more general definition of a dipole may be "any charge distribution whose first non-vanishing electrostatic moment is the dipole moment". The multipole expansion is a means of expressing an arbitrary charge distribution as a series in spherical harmonics. The first moments are (ignoring normalization terms): First moment (Monopole or Total charge): A scalar given by the integral over of charge density over all space, or the sum of charges in the discrete case (point charges). Second moment (Dipole): A vector (3x1) given by the integral over (charge density)*(position), or the sum or position*charge for point charges. Third moment (Quadrapole): A second rank tensor (3x3) given by the integral over (charge density)*(outer product of position), or the analgous sum for point charges. In general, the nth moment will be an (n-1)th order tensor (although typically fewer terms than 3^(n-1) are needed to describe the moment). As with many series representations, an approximation can be made by truncating the series at some value. In this case, we may approximate the electrostatic field outside of the charge distribution by taking only the leading moments. As the contribution to the potential falls off faster (with respect to distance from the centre of expansion) for higher order moments the far-field effects may be captured with a relatively small number of terms. Of course, the caveat that needs mentioning is that short range interactions should not generally be treated using an expansion; the expansion strictly holds only for points in space outside the bounding sphere of the charge distribution (centred at the point of expansion), and accurate representation in the near-field may require many terms. Classical Electrodynamics, by Jackson (Wiley, 1999 for 3rd Ed.) is a great reference for this, and all things electrostatic. Chapter 4 has an exposition on the multipole expansion. ======================================================================== David F. Green Assistant Professor http://www.ams.sunysb.edu/~dfgreen/ Applied Mathematics and Statistics Stony Brook University Office: +1-631-632-9344 Math Tower, Room 1-117 Mobile: +1-617-953-3922 Stony Brook, NY 11794-3600 Fax: +1-631-632-8490 ======================================================================== Marc Baaden baaden.^^.smplinux.de wrote: > Sent to CCL by: Marc Baaden [baaden%a%smplinux.de] > > David, > > thank you for the very enlightening comments, suggestions and references. > > >>>>"David F. Green dfgreen:+:ams.sunysb.edu" said: > > >> The standard definition of the dipole moment holds regardless of the net > >> charge. [..] > > Hmm, I'd like to ask: what is the standard definition of a molecular dipole ? > > In several textbooks I found definitions along the line of "A dipole is a > pair of electric charges of equal magnitude but opposite polarity [..]" > which *implies* that the net charge is zero. This was also IMHO the "classical" > and somewhat intuitive definition. > > I guess the second moment definition as integral over charge times position > vector would be a better/more general definition. But what makes > these definitions equivalent or allows to expand from one to the other ? > (The first definition a priori breaking down for charged species) > > Also there must be a rationale to discard other definitions, eg one could > dream up a definition of a molecular dipole as sum of all bond dipoles ? > > Are there seminal references on this ? > > Thanks, > Marc Baaden > From owner-chemistry@ccl.net Fri Nov 4 13:50:01 2005 From: "TJ O Donnell tjo:-:acm.org" To: CCL Subject: CCL: Dipole Moments and Molecular Fragments Message-Id: <-29883-051104132317-17683-TukIIG0iMICvjLbZlYO7iA*_*server.ccl.net> X-Original-From: "TJ O'Donnell" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Fri, 04 Nov 2005 10:23:01 -0800 MIME-Version: 1.0 Sent to CCL by: "TJ O'Donnell" [tjo.^^.acm.org] I agree, in particular: > I think chemists have attached too much > significance to the undeniable separation of charge that exists between > bonded atoms of different electronegativities, mainly because there was > no way to demonstrate that these charge separations were not necessarily > quantitatively or qualitatively different from any others that might be > defined for the system. There are many molecular properties that are successfully computed using fragments, whether they be atom fragments, bond fragments or group fragments - clogp, heats of formation, dipole moments, etc. The choice of fragments is arbitrary and similar results can be obtained using other fragments. For example, clogp is famously computed using group fragments, such as those defined by Al Leo, et. al. But it can be computed just as well (IMHO) using atom fragments. One can argue statistics about the fit to clogp for one method compared to the other, but the results of such arguments only lead to a decision about which method is more predictive/useful, not which method is more correct nor which more accurately represents some underlying physics. Any molecular property is truly a property unique to that particular molecule and (never?) uniquely attributable to any sums of fragments. Fragment analyses are always arbitrary, albeit superbly practical and useful. One exception might be molecular weight, which is uniquely attributable to a sum of atomic weights. But this might be considered more of a definition and it surely DOES reveal something about the underlying physics. It arises from the fact/observation that the nuclear mass of one atom is unaffected by that of neighboring atoms. Electrons don't behave like that, as we all know. Otherwise chemistry would be simply physics. TJ O'Donnell gNova Scientific Software http://www.gnova.com/ Phil Hultin hultin.:.cc.umanitoba.ca wrote: > The question about dipole moments of charged species is related to > another issue, which is somewhat of a hobby-horse of mine. > > > > In organic chemistry and biochemistry particularly, structural and > mechanistic rationales are often based on the idea of “fragment dipoles” > and their interactions with one another. In small molecules these are > usually dipoles said to be associated with polar covalent bonds, while > in proteins the so-called helix dipole is another example. > > > > For many years I accepted the idea that “intramolecular dipole-dipole > repulsions” were good explanations for all kinds of phenomena, but I am > in serious doubt about that idea now. When you start to dissect the > overall dipole moment of a molecule, you enter into the same kind of > origin-dependence that you see in ions. What makes the arbitrary choice > of a bond dipole or a helix dipole more significant than the infinitude > of other point-to-point dipoles that could be defined within the > molecular charge envelope? I think chemists have attached too much > significance to the undeniable separation of charge that exists between > bonded atoms of different electronegativities, mainly because there was > no way to demonstrate that these charge separations were not necessarily > quantitatively or qualitatively different from any others that might be > defined for the system. > > > > We have looked at charge distributions to seek evidence for fragment > dipoles and their interactions, and we haven’t seen anything convincing. > Do others have any opinions on this? > > > > Dr. Philip G. Hultin > > Associate Professor of Chemistry, > > University of Manitoba > > Winnipeg, MB > > R3T 2N2 > > hultin]^[cc.umanitoba.ca > > http://umanitoba.ca/chemistry/people/hultin > > > From owner-chemistry@ccl.net Fri Nov 4 14:46:01 2005 From: "IEJMD iejmd^yahoo.com" To: CCL Subject: CCL: IEJMD special issue dedicated to Professor Lemont B. Kier Message-Id: <-29884-051104134216-21869-r2CBBB8Ehq66vRJ9O9nSow+*+server.ccl.net> X-Original-From: IEJMD Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 4 Nov 2005 09:40:10 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: IEJMD [iejmd%yahoo.com] First Circular - Call for Papers Internet Electronic Journal of Molecular Design, http://www.biochempress.com Special Issue - dedicated to Professor Lemont B. Kier on the occasion of the 75-th birthday. You are invited to contribute a paper to the special issue of the Internet Electronic Journal of Molecular Design, http://www.biochempress.com, dedicated to Professor Lemont B. Kier. If you decide to contribute a paper, please note these important deadlines: - Title of the manuscript and authors submitted by Email to iejmd() yahoo.com : December 1st, 2005 - Manuscript submitted by Email to iejmd() yahoo.com : March 1st, 2006 All papers submitted for publication in the Internet Electronic Journal of Molecular Design must be prepared by using the Word template file IEJMD_template.doc, available from http://www.biochempress.com or from ftp://biochempress.com/Docs/IEJMD_template.doc The topic of the paper can be any original contribution regarding computer-assisted molecular design applications in chemistry, biochemistry, biology, chemical and pharmaceutical industry, including: - Computer-aided organic synthesis - Chemical structure and reactivity investigated with molecular mechanics, quantum chemistry, and molecular dynamics methods - Definition, calculation and evaluation of novel structural descriptors - Chemical database searching, clustering, similarity and diversity measure - Prediction of physico-chemical properties with Quantitative Structure-Property Relationships (QSPR) - Quantitative Structure-Activity Relationships (QSAR) models for biological activity, toxicity, mutagenicity, and carcinogenicity - Prediction of chromatographic retention parameters and design of stationary phases for chromatography - Modeling of bioorganic compounds, such as proteins, enzymes, and nucleic acids - New algorithms for modeling chemical and biochemical phenomena, such as global optimization methods, simulated annealing, neural networks, genetic algorithms, ant colony algorithm - Design of special materials, catalysts, high energy compounds, polymers, molecular machines If you have any questions regarding this special issue, please contact me by E-mail at: iejmd() yahoo.com If you want to contribute a paper, but need more time for the submission, send an E-mail with an estimated time of submission. Best regards, Ovidiu Ivanciuc ###################################### Ovidiu Ivanciuc Sealy Center for Structural Biology, Department of Human Biological Chemistry & Genetics, University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555-0857 USA __________________________________ Yahoo! Mail - PC Magazine Editors' Choice 2005 http://mail.yahoo.com From owner-chemistry@ccl.net Fri Nov 4 17:01:00 2005 From: "Robinson, James James.Robinson[a]evotec.com" To: CCL Subject: CCL: Dipole moment calculation from non-zero charge distribution, just a thought. Message-Id: <-29885-051104165958-30396-AWtiKxgMYgq4JhK82gvCDg,;,server.ccl.net> X-Original-From: "Robinson, James" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Date: Fri, 4 Nov 2005 21:59:44 -0000 MIME-Version: 1.0 Sent to CCL by: "Robinson, James" [James.Robinson],[evotec.com] It is quite easy to measure the dipole moment of a neutral molecule in a non-polar solvent. One makes up differing concentrations of solute in solvent, measure dielectric constants and density/refractive index, do measurements and some regression analysis and out comes dipole moment. A paper related to this is Halverstadt and Kulmer, JACS, 1942, 64, 2988-2992. Is it possible to measure the dipole moment of an ion, cationic or anionic, in solution? I don't know. I am sure that implicit and explicit solvation calculations will correlate with measured values for neutral moities. Until it becomes possible to actually have experimental values for ionic moiety dipole moment in solution, are ab-initio calculations of charged dipole moment in solution simply a leap into the unknown? I understand that ions behave in a particular manner in solution, I am a fan of ionic strength - but that is an aside. I thought models should be validated by empirical evidence. How does one describe the dipole of an anion in solution? James J Robinson -----Original Message----- > From: owner-chemistry[]ccl.net [mailto:owner-chemistry[]ccl.net] Sent: 04 November 2005 10:15 To: Robinson, James Subject: CCL: Dipole moment calculation from non-zero charge distribution Sent to CCL by: "Marc Baaden" [baaden^^^smplinux.de] Dear CCL readers, I am looking for a formular/recipe to calculate the dipole moment for a charged molecule. In that case my guess is that you first have to "factor out"/remove the monopole, but I couldn't find a precise formula for this case. In one textbook the dipole moment is simply given as the integral over r*p(r) where r is the position of the charge and p(r) the charge density at r. But for a charge distribution with net charge, this does not correspond to a separation of equal amounts of positive and negative charge ... .. as a naive suggestion, I could imagine calculating the geometrical centre of all negative charge and of all positive charge, remove the monopole charge from those and then calculate the dipole moment for this. But I would like confirmation (maybe even a reference or textbook) that explicitly handles this case. Thanks in advance, Marc Baaden NB: maybe I should add that this is for a classic (molecular mechanics) model of a protein with fixed point charges. The protein is charged due to the protonation states of its ionizable residues. Also in this context, is there a software package that can take a charge distribution (ideally a PDB file with charges in the last column) and calculate monopole + dipole + octapole + hexadecapole moments for this ? -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baaden _ smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Nov 4 22:07:01 2005 From: "Zhao Yuan ccl%%mail.sioc.ac.cn" To: CCL Subject: CCL: how to find active site? Message-Id: <-29886-051104215707-4896-M2HCwVEcpP+IeOo9J5DctA]*[server.ccl.net> X-Original-From: "Zhao Yuan" Content-Type: Multipart/Alternative; boundary="------------Boundary-00=_I2MGG6G0000000000000" Date: Sat, 5 Nov 2005 10:11:06 +0800 MIME-Version: 1.0 Sent to CCL by: "Zhao Yuan" [ccl*|*mail.sioc.ac.cn] --------------Boundary-00=_I2MGG6G0000000000000 Content-Type: Text/Plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable Hi, Everyone!=0D =0D I will very appreciate if somebody lets me know how to find an active s= ite=0D > from a protein-ligand structure?=0D Thank you!=0D =0D Steven --------------Boundary-00=_I2MGG6G0000000000000 Content-Type: Text/HTML; charset="gb2312" Content-Transfer-Encoding: quoted-printable
Hi, Everyone!
 =20
  I will very appreciate if somebody lets me know how to f= ind an active site
from a protein-ligand structure?
  Thank you!
 
Steven
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