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 ?