From mauro@carbon.foodsci.unibo.it Mon Oct 13 09:50:30 1997 Received: from carbon.foodsci.unibo.it for mauro@carbon.foodsci.unibo.it by www.ccl.net (8.8.3/950822.1) id JAA02248; Mon, 13 Oct 1997 09:10:50 -0400 (EDT) Received: from localhost (mauro@localhost) by carbon.foodsci.unibo.it (8.7.5/8.7.3) with SMTP id PAA16006 for ; Mon, 13 Oct 1997 15:12:30 +0200 Date: Mon, 13 Oct 1997 15:12:14 +0200 (MET DST) From: "Mauro A. Cremonini" Reply-To: "Mauro A. Cremonini" To: Computer Chemistry List Subject: Heme calculations (SUMMARY) In-Reply-To: <199710102255.AA101664115@london.ks.uiuc.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Transfer-Encoding: QUOTED-PRINTABLE Some days ago I placed the following question: >Dear netters, >can anybody point me to some fundamental publication about ab intio >calculation of hemes? In particular I would be glad to know which basis >set is best suited for calculating spin delocalization from iron to heme. Here I enclose the answers I got. Thank you very much to all who aswered. Mauro =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 Mauro Andrea Cremonini, PhD Food Science and Technology Laboratory University of Bologna Via Ravennate 1020 - Cesena - Italy FAX:+39.547.382348 e-mail: mauro@carbon.foodsci.unibo.it 73 de IK4QIX =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=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3DSUMMARY STARTS HER= E=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D Dear Mauro, You may find some useful references reganding ab inito heme calculations in our paper: W.Nowak and J.-L.Martin, "Towards understanding of qunatum factors in small ligand geminate recombination to heme proteins", published in the proceedings of "Quantum Mech. Simul. Methods for Studying Biological Systems. Les Houches Workshop 1995 (Pub. 1996). Eds. D.Bicout, M.Field, Springer, Berlin, Germany; pp.257-270. These are somewhat old but anyhow may be useful for you. Please summarize responses. WIth kind regards, Wieslaw Nowak =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=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D >From rohmer@quantix.u-strasbg.fr Mon Oct 6 15:32:40 1997 Date: Mon, 6 Oct 1997 12:33:33 +0200 (DFT) From: rohmer@quantix.u-strasbg.fr To: mauro@carbon.foodsci.unibo.it Subject: Re: CCL:ab initio calculation on heme Dear Mauro, I did sometimes ago a series of ab initio calculations on the heme (and on other metalloporphyrins as well) We used double-zeta types basis sets (and even triple-zeta for the outer shells) Some references: REVIEW ARTICLE: Ab initio calculation of metalloporphyrins, A. Dedieu, M.-M. Rohmer, A. Veillard, Advances in Quantum Chemistry, P.O. Lowdin ed., Vol 16, p. 43, Academic Press, New York 1982. OTHER ARTICLES: =20 Oxygen binding to manganese porphyrin. An ab initio calculation. A. DEDIEU et M.M. ROHMER, J. Am. Chem. Soc., 99 (1977) 8050. =20 Electronic and structural aspects of the dioxygen complexes of metalloporphyrins. An ab initio study. A. DEDIEU, M.M. ROHMER, H. VEILLARD et A. VEILLARD, Nouv. J. Chim., 3 (1979) 653. =20 Electronic structure and properties of model oxy- and carboxy ferrous cytochrome P450 : comparison of semi-empirical and ab initio calculations. M.M. ROHMER et G.H. LOEW, Int. J. Quant. Chem., Quantum Biology Symposium, 6 (1979) 93. Theoretical studies of the structure of heme models. A. VEILLARD, A. DEDIEU et M.M ROHMER dans : Horizons of Quantum Chemistry (B. Pullman et K. Fukui eds.) D. Reidel, Holland, (1980) p. 197. =20 Electronic spectra of model oxy, carboxy P450 and carboxy heme complexes. G.H. LOEW et M.M. ROHMER, J. Amer. Chem. Soc., 102 (1980) 3655. Calculated ground-state properties and optical spectrum of model carbonylheme complexes. Z.S. HERMAN, G.H. LOEW et M.M. ROHMER, Int. J. Quant. Chem., Quantum Biology Symposium, 7 (1980) 137. Structure, spectra and function of model cytochrome P450. G.H. LOEW, Z.S. HERMAN, M.M. ROHMER, A. GOLDBLUM et A. PUDZIANOWSKI, Annals of the New-York Academy of Sciences, 367 (1981) 192. Structure and properties of a model of deoxyheme. An ab initio SCF calculation. M.M. ROHMER, A. DEDIEU et A. VEILLARD, Chem. Phys., 77 (1983) 449. Conformational preferences of the axial ligands in some metalloporphyrins. A theoretical study. M.M. ROHMER, A. STRICH et A. VEILLARD, Theoret. Chim. Acta, 65 (1984) 219. Electronic ground state of iron(II)porphyrin. Ab initio SCF and CI calculations and computed electron deformation densities. M.M. ROHMER, Chem. Phys. Letters, 116 (1985) 44. Electronic structure of metalloporphyrins. Ab initio CI Calcu- lations. M.M. ROHMER dans : Quantum Chemistry. The Challenge of Transition Metals and Coordination Chemistry. NATO ASI series 176, A. Veillard ed., Reidel (1986) 377. Photochemical cleavage of the metal-carbon bond in aluminium porphyrins : insights from ab initio calculations. M.M. ROHMER, Chem. Phys. Letters, 157 (1989) 207. A theoretical study of the electron density in iron(II) porphyrin bis(water). M.M. ROHMER, Inorg. Chem., 28 (1989) 4574. Photochemical cleavage of the metal-hydrogen bond in aluminium porphyrins: insights from ab initio calculations. M.M. ROHMER, A.VEILLARD, New. J. Chem. 15 (1991) 796. Best regards, Marie-Madeleine /-------------------------------------------------------------------\ | Dr. Marie-Madeleine Rohmer | | Laboratoire de Chimie Quantique, UPR 139 du CNRS, | | Universite Louis Pasteur 4, rue Blaise Pascal 67000 STRASBOURG | | Tel: (33)03.88.41.61.42 Fax: (33)03.88.61.20.85 | | e-mail : rohmer@quantix.u-strasbg.fr | \-------------------------------------------------------------------/ =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=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 >From gmercier@mail.med.upenn.edu Tue Oct 7 17:54:04 1997 Date: Tue, 07 Oct 1997 11:51:39 +0000 From: Gustavo Mercier To: mauro@carbon.foodsci.unibo.it Subject: porphyrin computations Hi! I have attached a text file with my references on porphyrins and metalloporphyrins. Check out the work by Dedieu and Veillard. For semiempirical stuff check Zerner. Good Luck Bye G. Mercier, Jr. M.D.,Ph.D. gmercier@mail.med.upenn.edu =20 1.=09Bhyrappa, P.; Young, J.K.; Moore, J.S.; Suslick, K.S. Dendrimer - Meta= lloporphyrins: Synthesis and Catalysis. J. Am. Chem. Soc. 118:5708-5711; 19= 96. 2.=09Binstead, R.A.; Crossley, M.J.; Hush, N.S. Modulation of Valence Orbit= al Levels of Metalloporphyrins by b - substitution: Evidence from Spectrosc= opic and Electrochemical Studies of 2 - Substituted Metallo - 5,10,15,20 - = tetraphenylporphyrins. Inorg. Ch em. 30:1259-1264; 1991. 3.=09Bockhorst, K.; Hoehn-Berlage, M.; Ernestus, R.-I.; Tolxdorff, T.; Hoss= man, K.-A. NMR - Contrast Enhancement of Experimental Brain Tumors with MnT= PPS: Qualitative Evaluation by In Vivo Relaxometry. Magn. Reson. Imaging 11= :655-663; 1993. 4.=09Bonnett, R. Nomenclature. In: D. Dolphin (Eds). The Porphyrins. Struct= ure and Synthesis, Part A., Vol. I. New York: Academic Press; 1978: pp. 1-2= 7. 5.=09Bos, M.A.; Kleigh, J.M. Determination of the Orientation Distribution = of Adsorbed Fluorophores Using TRIF. I. Theory. Biophys. J. 68:2566-2572; 1= 995. 6.=09Bos, M.A.; Kleijn, J.M. Determination of the Orientation Distribution = of Adsorbed Fluorophores Using TIRF. II. Measurements on Porphyrin and Cyto= chrome c. Biophys. J. 68:2573-2579; 1995. 7.=09Boucher, L.J. Manganese Porphyrin Complexes. Coord. Chem. Rev. 7:289-3= 29; 1972. 8.=09Case, D.A.; Karplus, M. Xa Multiple Scattering Calculations on Copper = Porphine. J. Am. Chem. Soc. 99:6182-6194; 1977. 9.=09Chen, B.M.L.; Tulinsky, A. Redetermination of the Structure of Porphin= e. J. Am. Chem. Soc. 94:4144-4150; 1972. 10.=09Collins, D.M.; Countryman, R.; Hoard, J.L. Stereochemistry of Low - S= pin Iron Porphyrins. I. Bis(imidazole) - a,b,g,d - tetraphenylporphinatoiro= n(III) Chloride. J. Am. Chem. Soc. 94:2066-2072; 1972. 11.=09Collman, J.P.; Gagne, R.R.; Reed, C.A.; Robinson, W.T.; Rodley, G. St= ructure of an Iron(II) Dioxygen Complex; A model for Oxygen Carrying Hemepr= oteins. Proc. Natl. Acad. Sci. USA 71:1326-1329; 1974. 12.=09Collman, J.P.; Hoard, J.L.; Kim, N.; Lang, G.; Reed, C.A. Synthesis, = Stereochemistry, and Structure - Related Properties of a,b,g,d - Tetrapheny= lporphinatoiron(II). J. Am. Chem. Soc. 97:2676-2681; 1975. 13.=09Dedieu, A.; Rohmer, M.-M.; Veillard, A. Oxygen Binding to Iron Porphy= rins. Ab Initio Calculations. In: B. Pullman, N. Goldblum (Eds). Metal - Li= gand Interactions in Organic Chemistry and Biochemistry, part 2., Dordrecht= - Holland: D. Reidel Publishing Co.; 1977: pp. 101-130. 14.=09Dedieu, A.; Rhomer, M.-M.; Veillard, A. Ab initio Calculations of Met= alloporphyrins. In: P.O. Lowdin (Eds). Advances in Quantum Chemistry, Vol. = 16. New York: Academic Press; 1982: pp. 43-95. 15.=09Dolphin, D. The Porphyrins. New York: Academic Press; 1978. 16.=09Dupuis, P.; Roberge, R.; Sandorfy, C. The Very Low Ionization Potenti= als of Porphyrins and the Possible Role of Rydberg States in Photosynthesis= =2E Chem. Phys. Lett. 75:434-437; 1980. 17.=09Fawwaz, R.; Bohdiewicz, P.; Lavalle, D.; Wang, T.; Oluwole, S.; Newho= use, J.; Alderson, P. Use of Metalloporphyrins in Diagnostic Imaging. Nucl.= Med. Biol. 17:65-72; 1990. 18.=09Fleischer, E.B.; Miller, C.K.; Webb, L. Crystal and Molecular Structu= res of Some Metal Tetraphenylporphines. J. Am. Chem. Soc. 86:2342-2347; 196= 4. 19.=09Freemantle, M. Porphyrin Syntheses have Geochemical and Environmental= Applications. C&EN September 26:25-27; 1994. 20.=09Fujii, H. Effects of the Electron - Withdrawing Power of Substituents= on the Electronic Structure and Reactivity in Oxoiron(IV) Porphyrin p-Cati= on Radical Complexes. J. Am. Chem. Soc. 115:4641-4648; 1993. 21.=09Furhop, J.-H.; Kadish, K.M.; Davis, D.G. The Redox Behavior of Metall= o Octaethylporphyrins. J. Am. Chem. Soc. 95:5140-5147; 1973. 22.=09Gassman, P.G.; Ghosh, A.; Alml=F6f, J. Electronic Effects of Peripher= al Substituents in Porphyrins: X - Ray Photoelectron Spectroscopy and Ab In= itio Self - Consistent Field Calculations. J. Am. Chem. Soc. 114:9990-10000= ; 1992. 23.=09Geraldes, C.F.G.C.; Sherry, A.D.; Vallet, P.; Maton, F.; Muller, R.N.= ; Mody, T.D.; Hemmi, G.; Sessler, J.L. Nuclear Magnetic Relaxation Dispersi= on Studies of Water Soluble Gadolinium(III) - Texaphyrin Complexes. JMRI 5:= 725-729; 1995. 24.=09Ghosh, A.; Almlof, J.; Gassman, P.G. Ab initio SCF studies of basis s= et effects in free base porphin. Chem. Phys. Lett. 186:113-118; 1991. 25.=09Gilbert, J.; Kassab, D.; Pawlow, J.H.; Santora, B.P.; Fiel, R.J.; Jos= hi, V.N.; Kozik, M. First Characterization of the Influence of Paramagnetic= Heteropoly Complexes of Tungsten on Relaxation Times of Water. Separation = of Various Contributions to Rela xivities. Inorg. Chem. 34:924-927; 1995. 26.=09Goff, H.; La Mar, G.N.; Reed, C.A. Nuclear Magnetic Resonance Investi= gation of Magnetic and Electronic Properties of "Intermediate Spin" Ferrous= Porphyrin Complexes. J. Am. Chem. Soc. 99:3641-3646; 1977. 27.=09Gouterman, M. Study of the Effects of Substitution on the Absorption = Spectra of Porphin. J. Chem. Phys. 30:1139-1161; 1959. 28.=09Gouterman, M. Optical Spectra and Electronic Structure of Porphyrins = and Related Rings. In: D. Dolphin (Eds). The Porphyrins. Physical Chemistry= , Part A., Vol. III. New York: Academic Press; 1978: pp. 1-165. 29.=09Hayashi, T.; Asai, T.; Hokazono, H.; Ogoshi, H. Dynamic Molecular Rec= ognition in Multifunctional Porphyrin and Ubiquinone. J. Am. Chem. Soc. 115= :12210-12211; 1993. 30.=09Hoard, J.L.; Cohen, G.H.; Glick, M.D. The Stereochemistry of the Coor= dination Group in an Iron(III) Derivative of Tetraphenylporphine. J. Am. Ch= em. Soc. 89:1992-1996; 1967. 31.=09Jiang, D.-L.; Aida, T. A dendritic iron porphyrin as a novel haemopro= tein mimic: effects of the dendrimer cage on dioxygen - binding activity. C= hem. Commun. :1523-1524; 1996. 32.=09Jones, D.H.; Hinman, A.S.; Ziegler, T. Density Functional Studies of = Iron(III) Porphines and Their One - Electron - Oxidized Derivatives. Inorg.= Chem. 32:2092-2095; 1993. 33.=09Kappas, A.; Drummond, G.S. Control of Heme Metabolism with Synthetic = Metalloporphyrins. J. Clin. Invest. 77:335-339; 1986. 34.=09Karlin, K.D. Metalloenzymes, Structural Motifs, and Inorganic Models.= Science 261:701-708; 1993. 35.=09Kellar, K.E.; Foster, N. Inorg. Chem. Inorg. Chem. 31:1353-1359; Rela= xation Enhancement of Water Protons by Manganese(III) Porphyrins: Influence= of Porphyrin Aggregation. 36.=09Kemp, D.S.; Petrakis, K.S. Synthesis and Conformational Analysis of c= is,cis - 1,3,5, - Trimethylcyclohexane - 1,3,5 - tricarboxylic Acid. J. Org= =2E Chem. 46:5140-5143; 1981. 37.=09Khandelwal, S.C.; Roebber, J.L. The Photoelectron spectra of tetraphe= nylporphine and some metallotetraphenylporphyrins. Chem. Phys. Lett. 34:355= -359; 1975. 38.=09Kirner, J.F.; Reed, C.A.; Scheidt, W.R. Stereochemistry of Manganese = Porphyrins. 2. The Toluene Solvate of a,b,g,d - Tetraphenylporphinatomangan= ese(II) at 20 and -175=B0 C. J. Am. Chem. Soc. 99:1093-1100; 1977. 39.=09Kitagawa, S.; Morishima, I.; Yonezawa, T.; Sato, N. Photoelectron Spe= ctroscopic Study on Metallooctaethylporphyrins. Inorg. Chem. 18:1345-1349; = 1979. 40.=09La Mar, G.N.; Walker, F.A. Proton Nuclear Magnetic Resonance and Elec= tron Spin Resonance Investigation of the Electronic Structure and Magnetic = Properties of Synthetic Low - Spin Ferric Porphyrins. J. Am. Chem. Soc. 95:= 1782-1796; 1973. 41.=09La Mar, G.N.; Eaton, G.R.; Holm, R.H.; Walker, F.A. Proton Magnetic R= esonance Investigation of Antiferromagnetic Oxo - Bridged Ferric Dimers and= Related High - Spin Monomeric Ferric Complexes. J. Am. Chem. Soc. 95:63-75= ; 1973. 42.=09La Mar, G.N.; Walker, F.A. Proton Nuclear Magnetic Resonance Studies = of High - Spin Manganese(III) Complexes with Synthetic Porphyrins. J. Am. C= hem. Soc. 97:5103-5107; 1975. 43.=09La Mar, G.N.; Walker (Jensen), F.A. Nuclear Magnetic Resonance of Par= amagnetic Metalloporphyrins. In: D. Dolphin (Eds). The Porphyrins. Physical= Chemistry, Part B., Vol. IV. New York: Academic Press; 1979: pp. 61-157. 44.=09Longuet - Higgins, H.C.; Rector, C.W.; Platt, J.R. Molecular Orbital = Calculations on Porphins and Tetrahydroporphine. J. Chem. Phys. 18:1174-118= 1; 1950. 45.=09Lyon, R.C.; Faustino, P.J.; Cohen, J.S.; Katz, A.; Mornex, F.; Colche= r, D.; Baglin, C.; Koenig, S.H. Tissue Distribution and Stability of Metall= oporphyrin MRI Contrast Agents. Magn. Reson. Med. 4:24-33; 1987. 46.=09McMillan, J.H.; Cox, G.G.; Kimler, B.F.; Spicer, J.S.; Batnitzky, S. = Mn[III] Uroporphyrin 1: A Novel Metalloporphyrin Contrast Agent for Magneti= c Resonance Imaging. Magn. Reson. Imaging 9:553-558; 1991. 47.=09Mercier, G.A., Jr. On The Molecular Spin Density and The Electrostati= c Potential as Determinants of the Relaxivity of Metalloporphyrins. Magn. R= eson. Imag. 13:807-817; 1995. 48.=09Munro, O.Q.; Bradley, J.C.; Hancock, R.D.; Marques, H.M.; Marsicano, = F.; Wade, P.W. Molecular Mechanics Study of the Ruffling of Metalloporphyri= ns. J. Am. Chem. Soc. 114:7218-7230; 1992. 49.=09Nelson, J.A.; Schmiedl, U. Porphyrins as Contrast Media. Magn. Reson.= Med. 22:366-371; 1991. 50.=09Ni, Y.; Marchal, G.; Petr=E9, C.; Yu, J.; Pfefferer, D.; Ebert, W.; S= emmler, W.; Baert, A.L. Paramagnetic Metalloporphyrins: Necrosis Specific C= ontrast Agents for Magnetic Resonance Imaging. In: Book of abstracts: 3rd S= cientific Meeting and Exhibition o f the International Society for Magnetic Resonance in Medicine and the 12th= Annula Meeting and Exhibition of the European Society For Magnetic Resonan= ce in Medicine and Biology, Vol. 2. Nice: ISMRM; 1995: pp. 1145. 51.=09Orti, E.; Bredas, J.L. Electronic Structure of Metal - Free Porphine:= A Valence Effective Hamiltonian Theoretical Investigation. Chem. Phys. Let= t. 164:247-252; 1989. 52.=09Ozette, K.; Leduc, P.; Palacio, M.; Bartoli, J.-F.; Barkigia, K.M.; F= ajer, J.; Battioni, P.; Mansuy, D. New Metalloporphyrins with Extremely Alt= ered Redox Properties: Synthesis, Structure, and Facile Reduction to Air - = Stable p - Anion Radicals of Zin c and Nickel b - heptanitroporphyrins. J. Am. Chem. Soc. 119:6442-6443; 199= 7. 53.=09Place, D.A.; Faustino, P.J.; Berghmans, K.K.; van Zijl, P.C.M.; Chesn= ick, A.S.; Cohen, J.S. MRI Contrast - Dose Relationship of Manganese(III) T= etra(4-Sulfonatophenyl) Porphyrin with Human Xenograft Tumors in Nude Mice = at 2.0 T. Magn. Reson. Imag. 10: 919-928; 1992. 54.=09Radonovich, L.J.; Bloom, A.; Hoard, J.L. Stereochemistry of Low - Spi= n Iron Porphyrins. II. Bis(piperidine) - a,b,g,d - tetraphenylporphinatoiro= n(II). J. Am. Chem. Soc. 94:2073-2078; 1972. 55.=09Rebek, J., Jr. Model Studies in Molecular Recognition. Science 235:14= 78-1484; 1987. 56.=09Robertson, D.E.; Farid, R.S.; Moser, C.C.; Urbauer, J.L.; Mulholland,= S.E.; Pidikiti, R.; Lear, J.D.; Wand, A.J.; DeGrado, W.F.; Dutton, P.L. De= sign and synthesis of multi - haem proteins. Nature 368:425-432; 1994. 57.=09Robinson, D.H.; Schmiedl, U.P.; Starr, F.L.; Nelson, J.A.; Malek, R. = Intravenous Manganese - Mesoporphyrin as a Magnetic Resonance Imaging Contr= ast Agent: An Experimental Model Using VX-2 Carcinoma in Rabbits. Acad. Rad= iol. 2:43-49; 1994. 58.=09Rodgers, K.R.; Reed, R.A.; Su, Y.O.; Spiro, T.G. Resonance Raman and = Magnetic Resonance Spectroscopic Characterization of the Fe(I), Fe(II), Fe(= III), and Fe(IV) Oxidation States of Fe(2-TMPyP)n+(aq). Inorg. Chem. 31:268= 8-2700; 1992. 59.=09Saini, S.K.; Jena, A.; Dey, J.; Sharma, A.K.; Singh, R. MnPcS4: a new= MRI contrast enhancing agent for tumor localisation in mice. Magn. Reson. = Imag. 13:985-990; 1995. 60.=09Schmiedl, U.P.; Nelson, J.A.; Starr, F.L.; Schmidt, R. Hepatic Contra= st - Enhancing Properties of Manganese - Mesoporphyrin and Manganese - TPPS= 4. Invest. Radiol. 27:536 - 542; 1992. 61.=09Schmiedl, U.P.; Nelson, J.A.; Robinson, D.H.; Michalson, A.; Starr, F= =2E; Frenzel, T.; Ebert, W.; Schuhmann-Giampieri, G. Pharmaceutical Propert= ies, Biodistribution, and Imaging Characteristics of Manganese - Mesoporphy= rin. A Potential Hepatobiliary Con trast Agent for Magnetic Resonance Imaging. Invest. Radiol. 28:925-932; 199= 3. 62.=09Sessler, J.L.; Burrell, A.K. Expanded Porphyrins. In: Topics in Curre= nt Chemistry, Vol. 161. Berlin, Heidelberg: Springer - Verlag; 1991: pp. 17= 7-273. 63.=09Sessler, J.L.; Mody, T.D.; Hemmi, G.W.; Lynch, V.; Young, S.W.; Mille= r, R.A. Gadolinium(III) Texaphyrin: A Novel MRI Contrast Agent. J. Am. Chem= =2E Soc. 115:10368-10369; 1993. 64.=09Shulman, R.G.; Glarum, S.H.; Karplus, M. Electronic Structure of Cyan= ide Complexes of Hemes and Heme Proteins. J. Mol. Biol. 57:93-115; 1971. 65.=09Silvers, S.J.; Tulinsky, A. The Crystal and Molecular Structure of Tr= iclinic Tetraphenylporphyrin. J. Am. Chem. Soc. 89:3331-3337; 1967. 66.=09Sontum, S.; Case, D.A. Xa Multiple Scattering Calculations on Copper,= Silver, and Gold Porphines. J. Phys. Chem. 86:1596-1606; 1982. 67.=09Sontum, S.F.; Case, D.A. Xa multiple scattering calculations on iron(= II) porphine. J. Chem. Phys. 79:2881-2892; 1983. 68.=09Spangler, D.; Maggiora, G.M.; Shipman, L.L.; Christoffersen, R.E. Ste= reoelectronic Properties of Photosynthetic and Related Systems. 2. Ab Initi= o Quantum Mechanical Ground State Characterization of Magnesium Porphine, M= agnesium Chlorin, and Ethyl Chlo rophyllide a. J. Am. Chem. Soc. 99:7478-7489; 1977. 69.=09Spangler, D.; Maggiora, G.M.; Shipman, L.L.; Christoffersen, R.E. Ste= reoelectronic Properties of Photosynthetic and Related Systems. 1. Ab Initi= o Quantum Mechanical Ground State Characterization of Free Base Porphine, C= hlorin, and Ethyl Pheophorbide a =2E J. Am. Chem. Soc. 99:7470-7477; 1977. 70.=09Stavrov, S.S. The Effect of Iron Displacement Out of the Porphyrin Pl= ane on the Resonance Raman Spectra of Heme Proteins and Iron Porphyrins. Bi= ophys. J. 65:1942-1950; 1993. 71.=09Sur, S.K.; Bryant, R.G. Spin - Lattice Relaxation Enhancement of Wate= r Protons by Ferric Porphyrins Complexed with Cyclodextrins and Fluoride Io= ns. J. Phys. Chem. 99:7172-7179; 1995. 72.=09Tulinsky, A.; Chen, B.M.L. The Crystal and Molecular Structure of Chl= oro - a,b,g,d - tetraphenylporphinato manganese(III). J. Am. Chem. Soc. 99:= 3647-3651; 1977. 73.=09Veillard, A. Ab Initio Calculations of Transition - Metal Organometal= lics: Structure and Molecular Properties. Chem. Rev. 91:743-766; 1991. 74.=09Wagner, R.W.; Johnson, T.E.; Lindsey, J.S. Soluble Synthetic Multipor= phyrin Arrays. 1. Modular Design and Synthesis. J. Am. Chem. Soc. 118:11166= -11180; 1996. 75.=09Yamamoto, T.; Matsumura, A.; Shibata, Y.; Yoshizawa, T.; Fujimori, H.= ; Yoshii, Y.; Nose, T.; Sakata, I.; Nakajima, S. Mn - Metalloporphyrin (ATN= -10) as A Tumor Targeting Contrast Agent for MR Imaging. In: Book of abstra= cts: 3rd Scientific Meeting and=20 Exhibition of the International Society for Magnetic Resonance in Medicine = and the12th Annual Meeting and Exhibition of the European Society for Magne= tic Resonance in Medicine and Biology, Vol. 2. Nice: ISMRM; 1995: pp. 1135. 76.=09Young, S.W.; Sidhu, M.K.; Qing, F.; Muller, H.H.; Neuder, M.; Zanassi= , G.; Mody, T.D.; Hemmi, G.; Dow, W.; Mutch, J.D.; Sessler, J.; Miller, R.A= =2E Preclinical Evaluation of Gadolinium (III) Texaphyrin Complex. A New Pa= ramagnetic Contrast Agent for Magn etic Resonance Imaging. Invest. Radiol. 29:330-338; 1994. 77.=09Yushmanov, V.E.; Imasato, H.; Tominaga, T.T.; Borissevitch, I.E.; Tab= ak, M. 1H NMR of Paramagnetic Metalloporphyrins: Solution Properties and In= teraction with Albumin. In: Book of abstracts: 3rd Scientific Meeting and E= xhibition of the International S ociety for Magnetic Resonance in Medicine and the12th Annual Meeting and Ex= hibition of the European Society for Magnetic Resonance in Medicine and Bio= logy, Vol. 2. Nice: ISMRM; 1995: pp. 1107. 78.=09Yushmanov, V.E.; Tominaga, T.T.; Borissevitch, I.E.; Imasato, H.; Tab= ak, M. Binding of Manganese and Iron Tetraphenylporphine Sulfonates to Albu= min is Relevant to Their Contrast Properties. Magn. Reson. Imag. 14:255-261= ; 1996. 79.=09Zerner, M.; Gouterman, M.; Kobayashi, H. Porphyrins. VIII. Extended H= =FCckel Calculations on Iron Complexes. Theoret. Chim. Acta (Berl.) 6:363-4= 00; 1966. =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= =3DEND OF SUMMARY=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 From ccl@www.ccl.net Mon Oct 13 11:30:24 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id LAA03089; Mon, 13 Oct 1997 11:23:45 -0400 (EDT) Received: from msuvx1.memphis.edu for tcundari@cc.memphis.edu by bedrock.ccl.net (8.8.6/950822.1) id LAA28855; Mon, 13 Oct 1997 11:23:34 -0400 (EDT) Received: from [141.225.145.9] by MSUVX1.MEMPHIS.EDU (PMDF V5.1-8 #16781) with SMTP id <01IOR6M7TMY88XX08Y@MSUVX1.MEMPHIS.EDU> for chemistry@ccl.net; Mon, 13 Oct 1997 10:23:27 CST Date: Mon, 13 Oct 1997 10:23:51 -0600 From: tcundari@cc.memphis.edu (Tom Cundari) To: chemistry@ccl.net Subject: ECPs in DFT Message-id: MIME-version: 1.0 Content-type: text/plain; charset="iso-8859-1" Content-transfer-encoding: quoted-printable Status: RO Content-Length: 5727 Fellow Net-tenders, Last week I inquired about ECPs in DFT. I got several responses, and info >from Georg Schreckenbach alerting me to an earlier question & summary in the CCL on a similar topic. Here are the responses. Sincerely, Tom Cundari ############################################################################## From: Mikhail Gloukhovtsev Tom, you can find some comparisons of DFT(B3LYP)/ECP results on Fe-containing species with those computed at other levels of theory in JPC, 1997, 101 A, 316. Best regards, Mikhail ############################################################################## From: "Dr. Heinz Schiffer" Hi Tom, have a look at : Christoph van Wuellen On the Use of Common Effective Core Potentials in Density Functional Calculations. I. Test Calculations on Transition-Metal Carbonyls Int. J. Quantum Chem. 58 (1996) 147-152 Hope this helps, Ciao Heinz ############################################################################## From: Tor Karlsen Hi, Here is another ref. on HF derived ECP's: C. V. Wullen, International Journal of Quantum Chemistry ,Vol 58, p.147-152 (1996) I guess the Hay et al. paper you refer to is the one in: J. Phys. Chem., 99, p.17085-17087 (1995) You should check the CCL archives because I think someone posted a similar request earlier this year. Yours Tor Karlsen ############################################################################## Date: Sun, 12 Oct 1997 12:35:39 +0200 (MET DST) From: Jauoad El Bahraoui Subject: RE: ECPs in DFT To: tcundari@msuvx2.memphis.edu MIME-version: 1.0 Hi! here you have some articles, about application of ECP in DFT Calculation for Transition Metals complexes: 1.- "Structural and Ab Initio Studies Of Ag-Ag Bonding In The Silver(I) Dimer Bis-M-(5,7-Dimethyl[1,2,4]Triazolo[1,5- A]Pyrimidine)Dinitrato Disilver(I)" J. El-Bahraoui, J. Molina Molina, M. A. Romero, J. M. Salas, M. Quiros,A. M. P Sanchez, R.Faure. J.Mol.Structure., 1995, 354, 189. 2.- "Binuclear Pt(II) Triazolopyrimidine Bridged Complexes. Preparation,Crystal Structure, NMR Spectroscopy and ab initio MO Investigation on The Bonding Nature of Pt(II)-Pt(II) Interaction in Model Compound {Pt2[NHCHN(C(CH2)(CH3))]4}." Jorge A. R. Navarro , M. Angustias Romero, Juan M. Salas, Miguel Quiros, Jaouad El-Bahraoui, Jose Molina and Bernhard Lippert. Inorg.Chem. 1996, 35, 7829-7835 3.- "Electronic Structure of Pi-Allyl-Palladium and Pd2x4 (X =3D Cl, Br, I) Models Systems : A Rhf And Density Functional Theory Study." J. El-Bahraoui, J. Molina Molina, D.Portal Olea J.Mol.Structure Accepted 4.-"Ab Initio Studies of Ag-Ag Bonding In The Silver(I) Dimer bis-Mu(5,7-Dimethyl[1,2,4]Triazolo[1,5-A]Pyrimidine)Dinitrato Disilver(I) : a RHF and Density Functional Study." J. El-Bahraoui, J. Molina Molina, D.Portal Olea J.Phys.Chem Accepted Hope this help sincerly, Jaouad El-Bahraoui ############################################################################## From: "Fred P. Arnold" Fred reports that "DeMon, from Dennis Salahub at U. Montreal contains a number of ECP with associated valence basis set + fitting functions." ############################################################################## From: schrecke@t12.lanl.gov (Georg Schreckenbach) Dear Tom, a while ago, I had posted a related question on the CCL about the transferability of HF potentials to DFT. Besides the reference by Hay et al., there is one more reference by Christian van Wuellen (in principle van W=FCllen, i.e., "Umlaut-U"), Int. J. Quant. Chem., 1996, 58, 147. They show that there is transferability. I attach the summary message as a separate mail (was on the CCL on Feb.20). It is quite instructive, I think. If you look, however, for people just using ECPs and DFT, then there are many since this stuff is readily available in programs like Gaussian. See, e.g., Martin Kaupp (I assume he will answer you as well ...), other people from Salahub's group (well, to be precise, Kaupp was with Salahub a while ago but isn't anymore), Frenking's group, ... Best regards from Georg ############################################################################## Georg also reports that a similar question & attendant summary was posted by him in February of this year, so that the archives will contain this info. ############################################################################## Bill Davis (davisw@drea.dnd.ca) reports that work on developing/applying ECPs to DFT is forthcoming from his Ph.D. work; so, be on the look-out for that. ############################################################################## Tom Cundari Department of Chemistry Associate Professor The University of Memphis e-mail:tcundari@cc.memphis.edu Memphis, TN 38152-6060 phone: 901-678-2629 FAX: 901-678-3447 http://www.chem.memphis.edu/umchem.html **** U of Memphis is searching for an Asst. Prof. of Computational Chemistry, contact me by email for details or see these URLs www.chem.memphis.edu/ccad.html www.chem.memphis.edu/ccletter.html **** From ccl@www.ccl.net Mon Oct 13 12:30:28 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id LAA03209; Mon, 13 Oct 1997 11:48:50 -0400 (EDT) Received: from chad.scs.uiuc.edu for godbout@chad.scs.uiuc.edu by bedrock.ccl.net (8.8.6/950822.1) id LAA29956; Mon, 13 Oct 1997 11:48:46 -0400 (EDT) Received: from localhost (godbout@localhost) by chad.scs.uiuc.edu (AIX4.2/UCB 8.7/8.7) with SMTP id KAA15428 for ; Mon, 13 Oct 1997 10:38:52 -0500 (CDT) Date: Mon, 13 Oct 1997 10:38:13 -0500 (CDT) From: Nathalie Godbout To: chemistry@ccl.net Subject: LANL2 ECP in G94 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I am looking for the references for the LANL2 ECPs found in Gaussian 94. I found these ECPs in the PNL site but when I look at the description, I see that they were designed to mimic the LANL2DZ family in Gaussian 9x. I couldn't find a reference in the Gaussian manual. Thank you for your help, Nathalie -------------------------------------------- | Nathalie Godbout | | University of Illinois at Urbana-Champaign | | 600 S. Goodwin Av. Box 23.6 | | Urbana, IL 61801 | -------------------------------------------- From ccl@www.ccl.net Mon Oct 13 19:30:26 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id SAA05629; Mon, 13 Oct 1997 18:32:47 -0400 (EDT) Received: from plato.chem.iupui.edu for morreale@chem.iupui.edu by bedrock.ccl.net (8.8.6/950822.1) id SAA11414; Mon, 13 Oct 1997 18:28:10 -0400 (EDT) Received: from localhost by plato.chem.iupui.edu (940816.SGI.8.6.9/MSU-2.04) id WAA07996; Mon, 13 Oct 1997 22:50:07 GMT Date: Mon, 13 Oct 1997 17:50:06 -0500 (EST) From: Antonio Morreale To: chemistry@ccl.net Subject: Drug design teaching materials? In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers I'm going to be incharge of teaching drug design for undergraduates. I would like yo know in some one can guide me in order to find some simple exercices on the net or some practical book. Thanks in advances. Antonio. From toukie@zui.unizh.ch Tue Oct 14 05:30:32 1997 Received: from zzmkgtw.zzmk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.8.3/950822.1) id FAA07794; Tue, 14 Oct 1997 05:22:04 -0400 (EDT) Received: by zzmkgtw.zzmk.unizh.ch; (5.65v3.2/1.3/10May95) id AA22640; Tue, 14 Oct 1997 07:18:44 +0100 Message-Id: <3.0.3.32.19971014072112.0068b0e8@highdent> X-Sender: toukie@highdent (Unverified) X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.3 (32) Date: Tue, 14 Oct 1997 07:21:12 +0100 To: chemistry@www.ccl.net From: "Hr. Dr. S. Shapiro" Subject: Seeking GA for regr. analysis Cc: toukie@zui.unizh.ch Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Seeking GA for regr. analysis Hr. Dr. S. Shapiro toukie@zui.unizh.ch From yubofan@guomai.sh.cn Tue Oct 14 11:30:37 1997 Received: from gm-email.guomai.sh.cn for yubofan@guomai.sh.cn by www.ccl.net (8.8.3/950822.1) id LAA09511; Tue, 14 Oct 1997 11:22:26 -0400 (EDT) Received: from ------ (others.guomai.sh.cn [202.96.206.116]) by gm-email.guomai.sh.cn (8.8.5/8.8.5) with ESMTP id XAA24792 for ; Tue, 14 Oct 1997 23:20:32 +0800 Message-ID: <344385B4.59A957B5@guomai.sh.cn> Date: Tue, 14 Oct 1997 22:46:12 +0800 From: Yubo Fan X-Mailer: Mozilla 4.01 [en] (Win95; I) MIME-Version: 1.0 To: Computational Chemistry List Subject: Need Job Samples of G94 with opt=QST2 or QST3 X-Priority: 3 (Normal) Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, Netters, I tried some new methods of Gaussian 94 for optimization of Transition States. I have some questions. When I use opt=QST3 option, can I use cartesian coordination for the three molecular specifications. If I can, could you please give some input file examples? Thank you very much Y. Fan -- ======================================================== FAN, Yubo Department of Chemistry E-Mail: yubofan@guomai.sh.cn Fudan University yubofan@fudan.edu.cn Shanghai, 200433 P. R. China Voice(86-21)65643978 ======================================================== From robert@pauli.utmb.edu Wed Oct 15 16:30:52 1997 Received: from nmr.utmb.edu for robert@pauli.utmb.edu by www.ccl.net (8.8.3/950822.1) id PAA17367; Wed, 15 Oct 1997 15:39:04 -0400 (EDT) Received: from pauli.utmb.edu by nmr.utmb.edu via SMTP (931110.SGI/930416.SGI.AUTO) for CHEMISTRY@www.ccl.net id AA00718; Wed, 15 Oct 97 15:41:14 -0600 Received: (from robert@localhost) by pauli.utmb.edu (950413.SUN.8.6.12/950213.SUN.AUTOCF) id OAA03396; Wed, 15 Oct 1997 14:38:40 -0500 Date: Wed, 15 Oct 1997 14:38:40 +0059 (CDT) From: Robert Fraczkiewicz Subject: vibration spectra from force-field calculations To: "Marc-Heinrich.Prosenc" Cc: CHEMISTRY@www.ccl.net In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Marc-Heinrich, On Wed, 15 Oct 1997, Marc-Heinrich.Prosenc wrote: > it would be kind if anyone could tell me if there exist a program that calculates > vibrational spectras from forcefields like MM2 or DISCOVER or HYPERCHEM .... for free ? > > do there any public domain routines exist, which are able to refine existing forcefields > like mm2 or amber when the IR-spectrum is given ? > CCL software archives contain free program RAMVIB that can do both calculate spectra and refine force fields (ftp://www.ccl.net/pub/chemistry/software/SGI/ramvib/). Although it works only with harmonic force fields, the program is pretty flexible in terms of force constant definitions. Harmonic force constants are second derivatives of potential energy; you can use your ingenuity to get (at least some) molecular mechanics parameters from these values. Best regards, Robert Fraczkiewicz From ccl@www.ccl.net Wed Oct 15 23:30:54 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id XAA20361; Wed, 15 Oct 1997 23:23:04 -0400 (EDT) Received: from jason02.u.washington.edu for mathomps@u.washington.edu by bedrock.ccl.net (8.8.6/950822.1) id XAA02876; Wed, 15 Oct 1997 23:23:04 -0400 (EDT) Received: from saul7.u.washington.edu (mathomps@saul7.u.washington.edu [140.142.82.2]) by jason02.u.washington.edu (8.8.4+UW97.07/8.8.4+UW97.05) with ESMTP id UAA13702 for ; Wed, 15 Oct 1997 20:23:03 -0700 Received: (from mathomps@localhost) by saul7.u.washington.edu (8.8.4+UW97.07/8.8.4+UW97.04) id UAA10621 for chemistry@ccl.net; Wed, 15 Oct 1997 20:23:03 -0700 (PDT) Date: Wed, 15 Oct 1997 20:23:03 -0700 (PDT) From: Mark Thompson Message-Id: <199710160323.UAA10621@saul7.u.washington.edu> To: chemistry@ccl.net Subject: WebLab Viewer question I'm having problems with WebLab viewer (from MSI) chopping off the last 2 atoms of XYZ files. Has anyone else experienced this? I'm using version 2.01 for Win95/NT. Just increasing the atom count at the top of the file by 2 does show all the atoms. Mark Thompson ps. This problem also happens with their buckytube.xyz sample file. pps. Other than this problem, this is a terrific structure viewer for the PC! From gabriele@palladium.enscm.fr Thu Oct 16 08:31:00 1997 Received: from cit.enscm.fr for gabriele@palladium.enscm.fr by www.ccl.net (8.8.3/950822.1) id HAA21922; Thu, 16 Oct 1997 07:58:45 -0400 (EDT) Received: from palladium.enscm.fr by cit.enscm.fr (AIX 4.1/UCB 5.64/4.03) id AA21240; Thu, 16 Oct 1997 13:48:35 +0200 Received: from localhost (gabriele@localhost) by palladium.enscm.fr.enscm.fr (8.8.7/950213.SGI.AUTOCF) via SMTP id DAA04257; Mon, 20 Oct 1997 03:04:16 GMT Date: Thu, 16 Oct 1997 14:04:16 +3500 (MDT;) From: Dr Gabriele VALERIO X-Sender: gabriele@palladium To: CHEMISTRY@www.ccl.net Cc: gabriele@palladium.enscm.fr Subject: Summary: Comp. Chem. & polymer science Message-Id: Summary: Comp. Chem. & polymer science Dear CCL, Sorry if I post this summary after a long time (about one month!)... finally here it is. I thank you very much all who responded. You will find below some of their answers. Gabriele My original question: > Dear colleagues, > > after a few years working on inorganic or metal compounds I am going to > study polymers and elastomers. My knowledge on the capabilities of the > computational tools in this field is therefore very restricted. > > In order to gain some general ideas I thought I could kindly ask all of > you any piece of information on this topic. I would like to know "what > can we do" with computational methods in polymer science. > > Here are some questions I have in mind: > > What properties can we calculate and How? > > With which methods? (Quantum chemical, classical force fields, > statistical, "macroscopic approach"...; static or dynamic approach...; > molecular-cluster, or periodic models...), and which programmes? > > What is the accuracy and the range of application for the different > methods? > What is the computational cost? > > > Any references of interesting books, reviews and papers related to CC on > polymers will also be appreciated. > > I hope to receive replies from people working in all the branches of the > polymer science and of the computational chemistry or molecular > modeling. Answers: 1--------------------------------------------------------------------------- From: Fenglou Mao The most famous commercial software which calcualte polymer's properties is MSI's cerius2. It can calculate twenty or thirty properties of polymer. You can go to the WWW address "http://www.msi.com" for more information. Sincerely Yours, FengLou Mao ******************************* ADD:Mr. FengLou Mao Peking University BeiJing P.R.China Tel:86-10-62751490 Fax:86-10-62751725 2-------------------------------------------------------------------------- From: Joel.Fried@UC.Edu (Joel R. Fried) I co-edit a journal on Computational & Theoretical Polymer Science (Elsevier). Molecular Simulations has excellent software for polymers (QSPR & force fields/builders to do MD simulations). There are a number of good books by Binder, Suter/Mattice, etc. Regards Joel Fried *********************************************************** Professor Joel R. Fried Director of the Ohio Molecular Computation and Simulation Network and Center for Computer-Aided Molecular Design Department of Chemical Engineering University of Cincinnati Cincinnati, Ohio 45221-0171 Tel. (513) 556-2767; sec. 556-2761 Fax. (513) 556-3473 email: jfried@alpha.che.uc.edu *********************************************************** 3------------------------------------------------------------------------- From: Dayong He Dear Gabriele, You are right. You will get more replies from the CCL community. http://www.polymer.uakron.edu/users/wlm/books.html A lot of publications, downloadable code of RIS. http://www.fos.su.se/physical/sasha/md_prog.html Downloadable code of MD http://rsc.anu.edu.au/RSC/NEMD.html Non-equ MD simulation codes, downloadable http://www.cooper.edu/engineering/chemechem/monte.html MC,MD related sites. http://flory.engr.utk.edu:80/mbsf/project/codelist.html list of codes. http://www.Cond-Mat.Physik.Uni-Mainz.de/ what they are doing. http://www.dl.ac.uk/CCP/CCP5/main.html A lot of free codes for MD, MC http://argo.cheme.cornell.edu/ A lot of shared codes for chain mol., MD, MC. ... in one of the recent issues of " Advances in Polymer Science", several of the leaders in this field published the review papers. Best wishes. Dayong. _____________________________________________________________________________ Dayong He Department of Chemistry Rutgers, The State University of New Jersey Piscataway, NJ 08855 Tel: (732)445-4619(o), Email: yong@rutchem.rutgers.edu _____________________________________________________________________________ 4------------------------------------------------------------------------- From: peter.willemsen@jotun.no Dear Gabriele, Our group is developing new hydrolysable polymers for use in=20 antifouling paints. We do not have significant experience in=20 moleculair modeling of polymers, but we are currently evaluating the=20 usefulness of computational chemistry for our research. We are=20 interested in property prediction, and modeling hydrolysis,=20 filmformation, and polymerisation mechanisms/rates. In addtion, we=20 intend to applly compoutational chemistry for our biocide development=20 (QSARs, 3D database queries etc.).=20 Some time ago I send some general questions to some mailing lists to=20 get some general information reg. polymer modeling. If you want I can=20 forward you the relevant answers.=20 The major conclusion was that most people recommend MSI's products=20 (especially Cerius2) for material engineering in general and for=20 polymer science in particular. Unfortunately their software is too=20 expensive for us, at least at this stage (they offered us a package=20 for around US$100.000!). I would be grateful if you could suggest us=20 more reasonable alternatives!!=20 Have you heard of MSI's Polymer Consortium, aiming to develop software= for polymer research? If you visit their website (at www.msi.com) you=20 can get probably more information. I would recommend to ask them for a= copy of their Polymer 2000 proposal which gives a good overview of the= current state of the art in polymer modeling. In addition you should try the following books: Jozef Bicerano: "Computational Modeling of Polymers.", Marcel=20 Dekker, Inc., New York, Basel, Hong Kong (1992), ISBN 0-8247-8438-3. Gelin, Bruce R "Molecular modeling of polymer structures and=20 properties" Hanser Publishers 1994 David Porter: "Group Interaction Modelling of Polymer=20 Properties.", Marcel Dekker, Inc., New York, Basel (1995), ISBN 0- 8247-9599-7. 5---------------------------------------------------------------------------- From: Lipkowitz A set of books dedicated to the topic of computational chemistry exists (Reviews in Computational Chemistry, Wiley Publishers). This series has introductory materials along with up to date reviews of varous computational methods. It lacks much in the way of polymer calculations, however. Nonetheless this series is directed towards the novice computational chemist and will serve as a good source of information for your needs. kenny lipkowitz 6----------------------------------------------------------------------------- From: Hogue, Pat As a practicing Materials Engineer for an aerospace company with a little familiarity with modeling, I can suggest some practical problems we face: 1. A new lubricant oil is available that has silicone atoms in the carbon backbone. Its volatility is superior to the best low vapor pressure (alkylated cyclopentane=ACP) oil now in use, and a good low temperature pour point. Another plus is an enthalpy of evaporation nearly twice that of the ACP. Its viscosity index and viscosity values are much the same as the ACP. What might its heat of adsorption to an iron oxide surface be compared to the ACP? Might it be more, or less, likely to decompose on hot iron (associated with sliding friction)? Can modeling predict viscosity, pressure/viscosity, temperature/viscosity, and viscosity/shear rate relationships? 2. One of our suppliers of printed wiring assemblies wants to use an organic activated (oxalic acid) flux (thickened with polyglycols). Is ethanolamine, d-limonene or some other cleaner best for solubelizing this mixture? 3. A variety of new solder alloys are becoming available that do not contain lead. Can modeling be used to predict the extent to which reliability degrading brittle intermetallic compounds will form at typical (125C) service temperatures? 7----------------------------------------------------------------------------- From: peter.willemsen@jotun.no Hi, The following reference might be of interest to you: Computer simulation of polymers. Madkour TM, Barakat AM. Polymer (Comp. & Theor. Polym. Sci. suppl.) 38(18), 35-46, 1997. Regards, Peter ================================================================ Gabriele VALERIO Laboratoire de Materiaux Catalytiques et Catalyse en Chimie Organique UMR 5618 ENSCM-CNRS Tel: 33-4-67144396 Ecole Nationale Superieure de Chimie Fax: 33-4-67144349 8, rue de l'Ecole Normale mailto:gabriele@palladium.enscm.fr 34296 Montpellier cedex 5 (FRANCE) http://palladium.enscm.fr/gabriele From PDu@synapticcorp.com Thu Oct 16 16:31:05 1997 Received: from S2 for PDu@synapticcorp.com by www.ccl.net (8.8.3/950822.1) id PAA24289; Thu, 16 Oct 1997 15:46:34 -0400 (EDT) Received: by S2 from localhost (router,SLMAILNT V2.2); Thu, 16 Oct 1997 11:40:16 Eastern Daylight Time Received: by S2 from S47.synapticcorp.com (38.232.56.47::mail daemon; unverified,SLMAILNT V2.2); Thu, 16 Oct 1997 11:40:15 Eastern Daylight Time Comments: Authenticated sender is From: "Ping Du" To: chemistry@www.ccl.net Date: Thu, 16 Oct 1997 08:42:42 +0000 Subject: Summary: 3D to 2D Conversion Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-Id: <19971016114016.006dae9d.in@S2> Thanks to those who responded to my question. >This question may have been posted before: is there software that >converts 3D models into 2D drawings that clearly display atoms and >bonds without overlapping, much like what a chemist would draw by >hand? -- Ping Du ================================================== From: victoria@acdlabs.com (Victoria Barclay) Hi Ping, If you have the 3D model in MOL format, you can import it to our chemical drawing package (ACD/ChemSketch), select "remove hydrogens" and then select the "2D clean" function. (The hydrogens will automatically be added afterwards.) If you'd like a copy of our latest demoCD, I'd be happy to send one. Best regards, Victoria ------------------- Victoria Barclay, Ph.D. Manager, Scientific Support Advanced Chemistry Development, Inc. Suite 605, 133 Richmond St. W., Toronto, Canada M5H 2L3 Voice: (416) 368-3435 Fax: (416) 368-5596 Toll-free: 800-304-3988 e-mail: victoria@acdlabs.com web: http://www.acdlabs.com ================================================== From: Dan Strahs Ligplot from Janet Thornton's group. Reference: Wallace AC. Laskowski RA. Thornton JM LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Engineering. 8(2):127-34, 1995 Feb. Abstract The LIGPLOT program automatically generates schematic 2-D representations of protein-ligand complexes from standard Protein Data Bank file input. The output is a colour, or black-and-white, PostScript file giving a simple and informative representation of the intermolecular interactions and their strengths, including hydrogen bonds, hydrophobic interactions and atom accessibilities. The program is completely general for any ligand and can also be used to show other types of interaction in proteins and nucleic acids. It was designed to facilitate the rapid inspection of many enzyme complexes, but has found many other applications. I don't know about the academic/industrial legality issues. ================================================== From: molmodel@banyu.co.jp Hi. I use "Consystant" as a 3D to 2D Conversion program. It is copyrighted by ExoGraphics. If you contact ExoGraphics.... P.O. Box 655 West Milford, NJ 07480 tel : 201-728-0188 fax : 201-728-0735 And I know that Sybyl(Tripos) also has 3D to 2D Converter. Toshiharu Iwama Molecular Modeling Group Banyu Pharmaceutical Co.,LTD. Okubo 3, Tsukuba 300-26, JAPAN E-mail molmodel@banyu.co.jp Tel +81-298-77-2000 Fax +81-298-77-2029 ================================================== From: "R. M. Macrae" I'm sure the maintainers of this site will respond to directly, but if not, check this out: http://schiele.organik.uni-erlangen.de/services/gif.html You can turn a variety of input formats into a 2D GIF or PNG file using this free service generously provided by the folks at Erlangen U. Regards Rod ------------------------------------------------- R. M. Macrae Muon Science Laboratory Institute of Physical and Chemical Research (RIKEN) e-mail: macrae@rikaxp.riken.go.jp (normal) and : macrae@rikmtl.riken.go.jp (MIME-encoded) Tel : (81) 484 62 1111 ext 3336 Fax : (81) 484 62 4648 ------------------------------------------------- ================================================== From: DOUGH@mdli.com Several programs will generate 2D layout of structures, including MDL Layout, Daylight Depict (on larger computers), and ExoGraphics Consystant and, I think, something from Cambridgesoft. Doug Henry MDLI ================================================== From: "Wolf-Dietrich Ihlenfeldt" Yes. See http://schiele.organik.uni-erlangen.de/services/gif.html A basic software package is even free (http://schiele.organik.uni-erlangem.de/cactvs/), and companies can purchase support to solve their local scripting/conversion problems (a number already did). -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu ================================================== From: jle@world.std.com (Joe M Leonard) There are various commercial codes to do this, but are you looking for those, or for non-commercial ones? If it's the former, I suggest MSI, Tripos, Daylight... If it's the latter, I would be interested in what you learn! Joe Leonard jle@world.std.com *~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* Ping Du, PhD Senior Scientist, Computational Chemistry Email: pdu@synapticcorp.com Synaptic Pharmaceutical Corporation Tel: (201) 261-1331x642 215 College Road, Paramus, NJ 07652 Fax: (201) 261-0623 *~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~*~* From pang@iris.chem.cuhk.edu.hk Sat Oct 18 02:31:35 1997 Received: from iris.chem.cuhk.edu.hk for pang@iris.chem.cuhk.edu.hk by www.ccl.net (8.8.3/950822.1) id BAA04202; Sat, 18 Oct 1997 01:50:24 -0400 (EDT) Received: by iris.chem.cuhk.edu.hk (940816.SGI.8.6.9/940406.SGI.AUTO) id NAA07439; Sat, 18 Oct 1997 13:51:10 +0800 Date: Sat, 18 Oct 1997 13:50:56 +0800 (HKT) From: Pang Siu Kwong To: chemistry@www.ccl.net Subject: heat of vaporization Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII How are you? I am a beginner of computational chemistry. Do you know is there any method and software to calculate the heat of vaporizaton of molecules, for examples, water, ammonia and hydrochloric acid. The heat of vaporizaton depends on intermolecular forces between molecules and they are dipole-dipole interaction(electrostatic term), van der Waals interaction and hydrogen bonding. Patrick Pang From SUNDIUS@phcu.helsinki.fi Sat Oct 18 10:31:28 1997 Received: from lumo.helsinki.fi for SUNDIUS@phcu.helsinki.fi by www.ccl.net (8.8.3/950822.1) id JAA05591; Sat, 18 Oct 1997 09:32:31 -0400 (EDT) Received: from phcu.helsinki.fi by phcu.helsinki.fi (PMDF V5.0-4 #1) id <01IOYIGSUM8W8ZE1PM@phcu.helsinki.fi>; Sat, 18 Oct 1997 16:32:08 +0300 Date: Sat, 18 Oct 1997 16:26:43 +0300 From: Tom Sundius U of Helsinki +358 9 1918339 Subject: Re: CCL:vibration spectra from force-field calculations In-reply-to: "Your message dated Wed, 15 Oct 1997 14:38:40 +0059 (CDT)" To: CHEMISTRY@www.ccl.net, Robert Fraczkiewicz Message-id: <01IOYIY3P7X28ZE1PM@phcu.helsinki.fi> MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=US-ASCII Content-transfer-encoding: 7BIT Content-transer-encoding: 7BIT References: Robert Fraczkiewicz wrote: > (ftp://www.ccl.net/pub/chemistry/software/SGI/ramvib/). Although it works > only with harmonic force fields, the program is pretty flexible in terms of > force constant definitions. Harmonic force constants are second derivatives > of potential energy; you can use your ingenuity to get (at least > some) molecular mechanics parameters from these values. This transformation is possible, but not quite trivial... (see, for instance, papers by K. Palmo and S. Krimm (University of Michigan)) +-----------------------------------------------------------------------+ ! Tom Sundius, Dept. of Physics Internet: Tom.Sundius@Helsinki.fi ! ! University of Helsinki, Finland sundius@phcu.helsinki.fi ! +-----------------------------------------------------------------------+ From chburger@aci.unizh.ch Sat Oct 18 12:31:30 1997 Received: from rzusuntk.unizh.ch for chburger@aci.unizh.ch by www.ccl.net (8.8.3/950822.1) id MAA06216; Sat, 18 Oct 1997 12:29:19 -0400 (EDT) Received: [from rzusgi.unizh.ch (chburger@rzusgi.unizh.ch [130.60.64.19]) by rzusuntk.unizh.ch (8.8.5/SMI-5.23) with SMTP id SAA02051 for ; Sat, 18 Oct 1997 18:29:18 +0200 (MET DST)] Date: Sat, 18 Oct 1997 18:29:18 +0200 (MDT) From: "Dr. Peter Burger" Reply-To: "Dr. Peter Burger" To: chemistry@www.ccl.net Subject: Turbomole & MO-visualization Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CClers is there any low-cost solution (non-Biosym) to plot MO's calculated with Turbomole? I have tried Viewmol (ver 2.0) but it seems to have problems with functions higher than d. Has anyone written a filter/inter- face for programs like Molden? Many thx in advance Peter ------------ Peter Burger Anorg.-Chem. Institut Universitaet Zuerich chburger@aci.unizh.ch From comartin@wicc.weizmann.ac.il Sat Oct 18 12:36:37 1997 Received: from winston.weizmann.ac.il for comartin@wicc.weizmann.ac.il by www.ccl.net (8.8.3/950822.1) id MAA06203; Sat, 18 Oct 1997 12:24:36 -0400 (EDT) Received: from localhost by winston.weizmann.ac.il; (5.65v3.2/1.1.8.2/28Jul95-1212AM) id AA14950; Sat, 18 Oct 1997 18:09:42 +0200 Date: Sat, 18 Oct 1997 18:09:42 +0200 (IST) From: "Jan M.L. Martin" X-Sender: comartin@winston.weizmann.ac.il To: "Stephan P.A. Sauer" Cc: CHEMISTRY@www.ccl.net Subject: Re: CCL:geometry of Anthracene In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 17 Oct 1997, Stephan P.A. Sauer wrote: > Hi, > > I am looking for experimentally or theoretically determined bondlengths > and bondangles of C10H14 anthracene. In all modesty :-) permit me to recommend J. M. L. Martin, J. El-Yazal, and J. P. Francois, ``Structure and vibrational spectrum of some polycyclic aromatic compounds studied by density functional theory. I. Naphthalene, azulene, phenanthrene, and anthracene'', Journal of Physical Chemistry 100, 15358-15367 (1996). Our best geometries in Cartesian coordinates can be downloaded from the WWW. There are refs. to expt. geoms. in the paper. JM --------------------------------------------------------------------------- dr. Jan M.L. Martin Senior Lecturer, Computational Chemistry Department of Organic Chemistry/Kimmelman Building, Room 262 Weizmann Institute of Science/Rechovot 76100/ISRAEL FAX +972(8)9344142 Phone +972(8)9342533 E-mail comartin@wicc.weizmann.ac.il *** research group WWW home page http://theochem.weizmann.ac.il/ *** ---- kol ha-olam kulo gesher tzar me'od, v'ha-ikar lo l'hitpached k'lal ---