From rswenson@magnus.acs.ohio-state.edu Sat Sep 9 10:59:36 1995 Received: from top.magnus.acs.ohio-state.edu for rswenson@magnus.acs.ohio-state.edu by www.ccl.net (8.6.10/950822.1) id KAA23284; Sat, 9 Sep 1995 10:54:56 -0400 Received: from by top.magnus.acs.ohio-state.edu (8.6.10/4.940426) id KAA04821; Sat, 9 Sep 1995 10:54:52 -0400 Message-Id: <199509091454.KAA04821@top.magnus.acs.ohio-state.edu> X-Sender: rswenson@magnus.acs.ohio-state.edu Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Sat, 09 Sep 1995 10:50:32 -0400 To: chemistry@www.ccl.net From: rswenson@magnus.acs.ohio-state.edu (Dick Swenson) Subject: Amber force field parameters X-Mailer: I have been attempting some molecular mechanical calculations using the AMBER force field utilizing the Hyperchem software on the small molecule flavin mononucleotide within certain flavoproteins. Attempts to perform these calculations while including the FMN cofactor generates a series of error messages due to the lack of parameters within the amber89 force field parameter sets, my most recent set. Does anyone have values for the following bonds, bends, angles or can you tell me how to estimate them? Also, I am somewhat confused about the correct atom type assignment for the carbon atoms for the central pyrazine ring of the isoalloxazine ring. Should they be CA, CB or CM? (The following parameters would be needed for the CM atom type for the carbon atoms bridging the pyrazine and pyrimidine rings and the CA atom type for the carbon atoms bridging the o-xylene and pyrazine rings as Hyperchem assigns them.) Thanks for the help. Stretch parameter for: type NC-CM type CA-N* Bend parameter for: types NC-CM-CM types NC-CM-N* types NC-CM-C types NC-CA-CA types CA-NC-CM types CA-CA-N* types CA-N*-CM types CA-N*-CT Torsion parameter for: types C-NC-CM-CM types C-NC-CM-N* types C-CM-NC-CA types CA-CA-N*-CM types CA-CA-N*-CT types CM-CM-NC-CA From arthur@csb0.IPC.PKU.EDU.CN Sat Sep 9 21:59:44 1995 Received: from csb0.IPC.PKU.EDU.CN for arthur@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.6.10/950822.1) id VAA26782; Sat, 9 Sep 1995 21:48:04 -0400 Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA07009; Sun, 10 Sep 95 09:34:19 -0700 Date: Sun, 10 Sep 1995 09:34:18 -0700 (PDT) From: Arthur Wang To: CCL mailing list Subject: Summary of Calculation of LogP Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, everyone! Last week I put forward the query for references of calculation of LogP and I got a few of very helpful answers. I should thank all who have given their kind hands. Here is the summary. Regards, Arthur Wang +===========================================================+ | | | Arthur Wang Doctoral Candidate | | | | Molecular Design Lab | | Institute of Physical Chemistry, Peking University | | Beijing 100871, P.R.China | | | | E-mail: arthur@ipc.pku.edu.cn | | Tel: 86-10-2501490 Fax: 86-10-2501725 | | WWW: http://www.ipc.pku.edu.cn/arthur/homepage.html | | | +===========================================================+ ************************SUMMARY OF CALCULATION OF LOGP*********************** Piece One: ----------------------------------------------------------------------------- From: vis@gensia.com In response to your enquiry: There have been two recent comparisons of available methods. (i) Viswanadhan et al, J. Comp. Chem. (1993) 14, 1019-1026. (ii) Moriguchi, I., et al Chem. Pharm. Bull., (1994), 42, 976. A critique of the second review has also been published. Leo, A. J., Chem. and Pharm. Bull., (1995), 43, 512. After the pioneering work of Hansch and Leo on substituent constants for 'Log P' (or lipophilicity), there have been several atttempts to develop methods simpler (such as the use of 'atomic' fragments, pioneered by Ghose and Crippen) and more complex (using information from Quantum Chemical calculations, such as the BLOGP method developed by N. Bodor and associates). Rekker's work on lipophilicity is highly notable as well. References for all these works may be found in the two references given above. We have developed the 'atomic' method much further, which is as yet unpublished. I believe several software companies are also developing newer versions & approaches and I am sure you will hear from them. ----------------------------------------------------------------------------- Piece Two: ----------------------------------------------------------------------------- From: jordi@stark.udg.es (Jordi Mestres) Here you will find enclosed some references on the calculation of Molecular Lipophilicity Potentials based on the atomic partition of the total molecular LogP contribution. Sincerely, Jordi -------------------------------------------------------------------------- 1 Ghose, A.K. and Crippen, G.M., J. Comput. Chem. 9 (1988) 80. 2 Furet, P., Sele, A. and Cohen, N.C., J. Mol. Graph. 6 (1988) 182. 3 Viswanadhan, V.N., Ghose, A.K., Revankar, G.R. and Robins, R.K., J. Chem. Inf. Comput. Sci. 29 (1989) 163. 4 Croizet, P., Langlois, M.H., Dubost, J.P., Braquet, P., Audry, E., Dallet, Ph. and Colleter, J.C., J. Mol. Graph. 8 (1990) 153. 5 Kantola, A., Villar, H.O. and Loew, G.H., J. Comput. Chem. 12 (1991) 681. 6 Heiden, W., Moeckel, G. and Brickmann, J. J. Comput.-Aided Mol. Design 7 (1993) 503. 7 Gaillard, P., Carrupt, P.-A., Testa, B. and Boudon, A., J. Comput.-Aided Mol. Design 8 (1994) 83. 8 Rozas, I., Du, Q. and Arteca, G.A., J. Mol. Graph. 13 (1995) 98. 9 Kurochkina, N. and Lee, B., Protein Engineering 8 (1995) 437. 10 Bone, R.G.A. and Villar, H.O., J. Mol. Graph. 13 (1995) 201. -------------------------------------------------------------------------- -------------------------------------------------------------------------- Piece Three ------------------------------------------------------------------------------ From: doyle@gibbs.oit.unc.edu (Donald Doyle) This was recently reviewed by Albert J. Leo. See Chem. Rev. vol.93, pp1281-1306 (June, 1993). ------------------------------------------------------------------------------ Piece Four ------------------------------------------------------------------------------ From: "Konrad, IRBM Chemistry, +39-6-91093606" Below is a list of log P refs which I have in my database. See chapters 4-5 in reference #13 for a good review of log P calculation methods. I you find these references useful and best of luck to you in developing your log P prediction method. (1) Dearden, J. C.; Bresnen, G. M. The measurement of partition coefficients. Quant. Struct.-Act. Relat. 1988, 7, 133-144. (2) Essex, J. W.; Reynodls, C. A.; Richards, W. G. Theoretical determination of partition coefficients. J. Am. Chem. Soc. 1992, 114, 3634-3639. (3) Ghose, A. K.; Pritchett, A.; Crippen, G. M. Atomic physicochemical parameters for three dimensional structure directed quantitative structure-activity relationships III: modelng hydrophobic interactions. J. Comput. Chem. 1988, 9, 80-90. (4) Koehler, M. G.; Grigoras, S.; Dunn, W. J., III The relationship between chemical structure and the logarithm of the partition coefficient. Quant. Struct.-Act. Relat. 1988, 7, 150-159. (5) Moriguchi, I.; Hirono, S.; Liu, Q.; Nakagome, I.; Matsushita, Y. Simple method of calculating octano/water partition coefficient. Chem. Pharm. Bull. 1992, 40, 127-130. (6) Moriguchi, I.; Hirono, S.; Nakagome, I.; Hirano, H. Comparison of reliability of log P values for drugs calculated by several methods. Chem. Pharm. Bull. 1994, 42, 976-978. (7) Richards, N. G. J.; Williams, P. B.; Tute, M. S. Empirical methods for computing molecular partition coefficients. I. Upon the need to model the specific hydration of polar groups in fragement-based approaches. Int. J. Quantum Chem.: Quantum Biology Symposium 1991, 18, 299-316. (8) (8) Richards, N. G. J.; Williams, P. B.; Tute, M. S. Empirical methods of computing molecular partition coefficients: II. Inclusion of conformational flexibility within fragment-based approaches. Int. J. Quantum Chem. 1992, 44, 219-233. (9) Viswanadhan, V. N.; Reddy, M. R.; Bacquet, R. J.; Erion, M. D. Assessment of methods used for predicting lipophilicity: application to nuceolsides and nuceloside bases. J. Comput. Chem. 1993, 14, 1019-1026. (10) Bodor, N.; Gabanyi, Z.; Wong, C.-K. A new method for the estimation of partition coefficient. J. Am. Chem. Soc. 1989, 111, 3783-3786. (11) Bodor, N.; Huang, M.-J. Predicting parition coefficients for isomeric diastereoisomers of some tripeptide analogs. J. Comput. Chem. 1991, 12, 1182-1186. (13) Hansch, C.; Leo, A. Exploring QSAR: Fundamentals and Applications in Chemistry and Biology; American Chemical Society: Washington, DC, 1995. ------------------------------------------------------------------------------ Piece Five: ------------------------------------------------------------------------------ From: MARTIN@cmda.abbott.com I'll just send some names, probably you have seen the articles: Leo, Al; Rekker; Ghose & Crippen; Moriguchi; Klopmann; Brinkman--JCICS recently; maybe unpublished but the QM people doing solvation test their model on logP--C. Cramer, Klampt (COSMO program), Tim Clark; I hear that the Wavefront people have a model; Darvas in a CompuChem module; . . . ------------------------------------------------------------------------------ ******************************THE END****************************************