Outro Revisado por pares

Macroconformations

2008; American Chemical Society; Linguagem: Inglês

10.1002/9783527627233.ch4

ISSN

1520-5835

Autores

Hans‐Georg Elias,

Tópico(s)

Polynomial and algebraic computation

Resumo

Chapter 4 Macroconformations Hans-Georg Elias, Hans-Georg EliasSearch for more papers by this author Hans-Georg Elias, Hans-Georg EliasSearch for more papers by this author Hans-Georg Elias, Hans-Georg EliasSearch for more papers by this author Book Author(s):Hans-Georg Elias, Hans-Georg EliasSearch for more papers by this author First published: 11 March 2008 https://doi.org/10.1002/9783527627233.ch4 AboutPDFPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShareShare a linkShare onEmailFacebookTwitterLinkedInRedditWechat Summary The shape of an isolated macromolecule is determined by its molecular conformation, i.e. macroconformation which in turn depends on the type, proportion, and sequence of microconformations within the molecule. Isolated macromolecules and their associations may exist not only as loose coils but also as compact physical structures that resemble Euclidean bodies such as spheres, ellipsoids or rods. Physical structures of molecules and their assemblies as well as their static and dynamic properties can be simulated mathematically by molecular or atomistic modeling. The simplest chemical structure of a macromolecule is that of a long chain of identically interconnected chain units. The main problem for cyclic macromolecules in good solvents is the scarcity of experimental data for well-characterized high-molecular weight cyclic macromolecules. In the good solvent toluene, branching parameters of 3-arm and 12-arm poly-(styrene) s follow the theory for unperturbed chains although the chains of the arms are supposedly perturbed. Bibliography of Force Fields AMBER (Assisted Model Building and Energy Refinement): P.Weiner, P.A.Kollman, J.Comput. Chem. 2 (1981) 287; S.J. Weiner, P.A. Kollman, D.A. Case, U.C. Singh, C. Ghio, G. Algona, S.Profeta Jr., P. Weiner, J.Am.Chem.Soc. 106 (1984) 765; S.J. Weiner, P.A. Kollman, D.T. Nguyen, D.A. Case, J.Comput.Chem. 7 (1986) 230 (nucleic acids and proteins) CASWeb of Science®Google Scholar CHARMM (Chemistry of Harvard Macromolecular Mechanics): B.R.Brooks, R.E.Bruccoleri, B.D.Olafson, D.J.States, S.Swaminathan, M.Karplus, J.Comput.Chem. 4 (1983) 187 (nucleic acids and proteins) 10.1002/jcc.540040211 CASGoogle Scholar CFF91( Consistent Valence Force Field 1991): "Discover" program of Molecular Simulations, Inc. (formerly: Biosym, Inc.): (a) J.A. Mapic,, U. Dinur, A.T. Hagler, Proc.Natl.Acad.Sci.USA 85 (1988) 5350 (b) J.A. Mapic, M.-J. Hwang, T.P. Stockfisch, U. Dinur, M. Waldman, C.S. Ewig, A.T. Hagler, J.Comput.Chem. 15 (1994) 162 (c) M.-J. Hwang, T.P. Stockfisch, A.T. Hagler, J.Am.Chem.Soc. 116 (1994) 2515 10.1073/pnas.85.15.5350 Web of Science®Google Scholar CVFF (Consistent Valence Force Field): T. Halicioglu, M. Pound, Phys.Sta.Sol. [A] 30 (1975) 619; A.T. Hagler, S. Lifson, P. Dauber, J.Am.Chem.Soc. 101 (1979) 5122 10.1002/pssa.2210300223 CASWeb of Science®Google Scholar DISCOVER®: Computer program with AMBER, CVFF, CFF91, ESFF (Molecular Simulations, Inc., San Diego) (includes Biosym, Inc., since Fall 1996) Google Scholar DREIDING (in honor of A.S. Dreiding, University of Zurich): S.L. Mayo, B.D. Olafson, W.A.God- dard III, J.Phys.Chem. 94 (1990) 8897 (organic molecules and inorganic molecules of groups 1–3) 10.1021/j100389a010 CASWeb of Science®Google Scholar ECEPP: M.J. Sippl, G. Nemethy, H.A. Scheraga, J.Phys.Chem. 88 (1984) 6231 (biological macromolecules); ECEPP-05: Y.A. Arnautova, A. Jagielska, H.A. Scheraga, J.Phys.Chem. B 110 (2006) 5025 10.1021/j150669a035 CASWeb of Science®Google Scholar ESFF (Extensible Systematic Force Field): S. Shi, L. Yan, Y. Yang, J.Fisher-Shaulsky, T. Thacher, J.Comput.Chem. 24 (2003) 1059 10.1002/jcc.10171 CASWeb of Science®Google Scholar MM2/MMP2 (Molecular Mechanics): N.L. Allinger, J.Am.Chem.Soc. 99 (1977) 8127; U. Burkert, N.L. Allinger, Molecular Mechanics (ACS Monograph 177), Am.Chem.Soc., Washington, DC 1982; N.L. Allinger, J.Comput.Chem. 8 (1987) 581 (inorganic and organic molecules) 10.1021/ja00467a001 CASWeb of Science®Google Scholar OPLS (Optimized Potentials for Liquid Simulations): W.L. Jorgensen, J.Tirado-Rives, J.Am.Chem.Soc. 110 (1988) 1657 (proteins and nucleic acids). 10.1021/ja00214a001 CASWeb of Science®Google Scholar PCFF (extension of CFF for polymers): see CFF91(c) and H. Sun, S.J. Mumby, J.R. Maple, A.T. Hagler, J.Am.Chem.Soc. 116 (1994) 2978; H. Sun, J.Comput.Chem. 15 (1994) 752; H. Sun, Macromolecules 28 (1995) 701 10.1021/ja00086a030 CASWeb of Science®Google Scholar Literature to Chapter 4 Google Scholar 4.1 OVERVIEW: Polymers in Solution Google Scholar V.N. Tsvetkov, V.Ye. Eskin, S.Ya. Frenkel, Structure of Macromolecules in Solution, Butterworths, London 1970 Google Scholar H. Yamakawa, Modern Theory of Polymer Solutions, Harper and Rowe, New York 1971 Google Scholar H. Morawetz, Macromolecules in Solution, Interscience, New York, 2nd ed. 1975 Google Scholar W.C. Forsman, Ed., Polymers in Solution. Theoretical Considerations and Newer Methods of Characterization, Plenum, New York 1983 Google Scholar H. Fujita, Polymer Solutions, Elsevier, Amsterdam 1990 Google Scholar W.W. Graessley, Polymeric Liquids and Networks. Volume I, Structure and Properties, Garland Science, New York (2004) Web of Science®Google Scholar T.A. Witten (with P.A. Pincus), Structured Fluids: Polymers, Colloids, Surfactants, Oxford University Press, New York 2004 Google Scholar 4.3a MOLECULAR AND ATOMISTIC MODELING (general) Google Scholar D.M. Hirst, A Computational Approach to Chemistry, Blackwell, Oxford 1990 Google Scholar A. Aharony, D. Stauffer, Introduction to Percolation Theory, Taylor and Francis, Philadelphia, 2nd ed. 1993 Google Scholar J.M. Haile, Molecular Dynamics Simulation, Wiley, New York 1994 Google Scholar W.T. Coffey, Yu.P. Kalmykov, J.T. Waldron, Eds., The Langevin Equation. With Applications in Physics, Chemistry and Electrical Engineering, World Sci.Publ., River Edge (NY) 1996 Google Scholar D. Frenkel, B. Smit, Understanding Molecular Simulation: From Algorithms to Applications, Academic Press, San Diego 1996 Google Scholar M.F. Schlecht, Molecular Modeling on the PC, Wiley, New York 1998 Google Scholar K. Machida, Principles of Molecular Mechanics, Wiley, New York 1999 Google Scholar F. Jensen, Introduction to Computational Chemistry, Wiley, Chichester 1999 Google Scholar A.R. Leach, Molecular Modelling. Principles and Applications, Prentice-Hall, Englewood Cliffs (NJ), 2nd ed. 2001 Google Scholar K. Binder, D.W. Heermann, Monte Carlo Simulation in Statistical Physics. An Introduction, Springer, Berlin, 4th ed. 2002 10.1007/978-3-662-04685-2 Google Scholar C.J. Cramer, Essentials of Computational Chemistry. Theory and Models, Wiley, Chichester 2002 Google Scholar E. Lewars, Computational Chemistry. Introduction to the Theory and Applications of Molecular and Quantum Mechanics, Kluwer, Dordrecht 2003 Web of Science®Google Scholar A. Hinchliffe, Molecular Modelling for Beginners, Wiley, Chichester 2003 Google Scholar D.P. Landau, K. Binder, A Guide to Monte Carlo Simulations in Statistical Physics, Cambridge University Press, New York, 2nd ed. 2005 10.1017/CBO9780511614460 Google Scholar 4.3b MOLECULAR AND ATOMISTIC MODELING (polymers) Google Scholar K.F. Freed, Renormalization Group Theory of Macromolecules, Wiley, New York 1987 Google Scholar R.J. Roe, Ed., Computer Simulation of Polymers, Prentice Hall, Englewood Cliffs (NJ) 1991 Google Scholar J. Bicerano, Ed., Computational Modeling of Polymers, Dekker, New York 1992 Google Scholar E.A. Colbourn, Ed., Computer Simulation of Polymers, Longman, Harlow (Essex) 1994 Google Scholar B.R. Gelin, Molecular Modeling of Polymer Structures and Properties, Hanser, Munich 1994 Google Scholar C. Monnerie, U.W. Suter, Atomistic Modeling of Physical Properties, Adv.Polym.Sci. 116 (1994) 10.1007/BFb0080194 Web of Science®Google Scholar W.L. Mattice, U.W. Suter, Conformational Theory of Large Molecules. The Rotational Isomeric State Model in Macromolecular Systems, Wiley, New York 1994 Google Scholar K. Binder, Ed., Monte Carlo and Molecular Dynamics Simulations in Polymer Science, Oxford Univ. Press, New York 1995 10.1093/oso/9780195094381.001.0001 Google Scholar M. Rehahn, W.L. Mattice, U.W. Suter, Rotational Isomeric State Models in Macromolecular Systems, Adv.Polym.Sci. 131/132 (1997) 10.1007/BFb0050957 Google Scholar A. Grosberg, Theoretical and Mathematical Models in Polymer Research, Academic Press, San Diego (CA) 1998 Google Scholar H.-D. Höltje, W. Sippl, D. Rognan, G. Folkers, Molecular Modeling. Basic Principles and Applications, Wiley-VCH, Weinheim, 2nd ed. 2003 (mainly peptides, no synthetic polymers) Google Scholar M. Kotelyanskii, D.N. Theodorou, Simulation Methods for Polymers, Dekker, New York 2004 10.1201/9780203021255 Google Scholar V. Galiatsatos, Ed., Molecular Simulation Methods for Predicting Polymer Properties, Wiley, New York 2005 Google Scholar 4.4a and 4.5 LINEAR CHAINS: UNPERTURBED AND PERTURBED CHAINS Google Scholar J.G. Kirkwood, Macromolecules (Collected Works of JGK), Gordon and Breach, New York 1967 Google Scholar P.J. Flory, Statistical Mechanics of Chain Molecules, Interscience, New York 1969; reprint: Hanser, Munich 1989 10.1002/bip.1969.360080514 Google Scholar A.J. Hopfinger, Conformational Properties of Macromolecules, Academic Press, New York 1973 Google Scholar C. Williams, F. Brochard, H.L. Frisch, Polymer Collapse, Ann.Rev.Phys.Chem. 32 (1981) 433 10.1146/annurev.pc.32.100181.002245 CASWeb of Science®Google Scholar N. Madras, G. Slade, The Self-Avoiding Walk, Birkhäuser, Basel 1993; see also G. Slade, Random Walks, American Scientist 84 (1996) 146 Google Scholar C. Vanderzande, Lattice Models of Polymers, Cambridge University Press, New York 1997 Google Scholar L. Schäfer, Excluded Volume Effects in Polymer Solutions, Springer, Berlin 1999 10.1007/978-3-642-60093-7 Google Scholar E.J. Janse Van Rensburg, The Statistical Mechanics of Interacting Walks, Polygons, Animals and Vesicles, Oxford University Press, Oxford 2000 Google Scholar 4.4b WORMLIKE AND STIFF CHAINS Google Scholar V.N. Tsvetkov, Rigid Chain Polymers. Hydrodynamic and Optical Properties in Solution, Plenum, New York 1989 Google Scholar G.L. Brelsford, W.R. Krigbaum, Experimental Evaluation of the Persistence Length for Mesogenic Polymers; in A. Ciferri, Ed., Liquid Crystallinity in Polymers, VCH, Weinheim 1991, p. 61 Google Scholar F.E.Arnold, Jr., F.E. Arnold, Rigid-Rod Polymers and Molecular Composites, Adv.Polym.Sci. 117 (1994) 257 10.1007/BFb0021201 CASWeb of Science®Google Scholar H. Yamakawa, Helical Wormlike Chains in Polymer Solutions, Springer, Berlin 1998 Google Scholar 4.6 CYCLIC MACROMOLECULES Google Scholar J.A. Semlyen, Ed., Cyclic Polymers, Elsevier Sci.Publ., New York 1986 10.1007/978-94-009-4175-5 Google Scholar 4.7 BRANCHED MACROMOLECULES Google Scholar W.W. Graessley, Entangled Linear, Branched and Network Polymer Systems–Molecular Theories, Adv.Polym.Sci. 47 (1982) 67 10.1007/BFb0038532 CASWeb of Science®Google Scholar W.L. Mattice, Masses, Sizes, and Shapes of Macromolecules from Multifunctional Monomers, in G.R. Newkome, C.N. Moorefield, F. Vögtle, Eds., Dendritic Molecules. Concepts, Synthesis, Perspectives, VCH Verlag, Weinheim 1996, Chapter I Google Scholar 4.8 SCALING Google Scholar B.B. Mandelbrot, Fractals: Form, Chance and Dimensions, Freeman, New York 1977; The Fractal Geometry of Nature, Freeman, New York 1982 Google Scholar M.K. Kosmas, K.F. Freed, On Scaling Theories of Polymer Solutions, J.Chem.Phys. 69 (1978) 3647 10.1063/1.437073 CASWeb of Science®Google Scholar P.G. de Gennes, Scaling Concepts in Polymer Physics, Cornell Univ. Press, Ithaca, New York 1979 10.1021/ma60075a033 CASWeb of Science®Google Scholar L. Pietronero, E. Tosatti, Fractals in Physics, North Holland, Amsterdam 1986 Google Scholar K.R. Freed, Renormalization Group Theory of Macromolecules, Wiley, New York 1987 Google Scholar J. Des Cloizeaux, G. Jannink, Les Polymères en Solution: Leur Modélisation et Leur Structure, Les Éditions de Physique, Les Ulis Cedex (France) 1987; Polymers in Solution. Their Modelling and Structure, Clarendon Press, Oxford 1990 Google Scholar H.H. Kaye, A Random Walk Through Fractal Dimensions, VCH, Weinheim 1989 Google Scholar D. Avnir, The Fractal Approach to Heterogeneous Chemistry: Surfaces, Colloids, Polymers, Wiley, New York 1989 Google Scholar M. Takayasu, Fractals in the Physical World, Manchester Univ. Press, Manchester 1989 Google Scholar D.W. Schaefer, Polymers, Fractals, and Ceramic Materials, Science 243 (1989) 1023 10.1126/science.243.4894.1023 CASPubMedWeb of Science®Google Scholar A. Blumen, H. Schnörer, Fractals and Related Hierarchical Models in Polymer Science, Angew.Chem.Int.Ed.Engl. 29 (1990) 113; −, Angew.Chem. 102 (1990) 158 10.1002/anie.199001133 Web of Science®Google Scholar R.J. Creswick, H.A. Farach, C.P. Poole, Jr., Introduction to Renormalization Group Methods in Physics, Wiley, New York 1991 Google Scholar F.C. Moon, Chaotic and Fractal Dynamics. An Introduction for Applied Scientists and Engineers, Wiley, New York 1992 10.1002/9783527617500 Google Scholar References to Chapter 4 Google Scholar J. Boor, Jr., E.A. Youngman, J.Polym.Sci. A 4 (1966) 1861, Fig. 6 Google Scholar B.H. Stofer, PhD Thesis 4577, ETH Zürich 1970, Fig. 17 Web of Science®Google Scholar B.H. Stofer, H.-G. Elias, Makromol.Chem. 157 (1972) 245, Fig. 6 10.1002/macp.1972.021570124 CASWeb of Science®Google Scholar S.M. Aharoni, N.S. Murthy, Polym.Commun. 24 (1983) 132, Table 1 CASWeb of Science®Google Scholar N. Donkai, H. Inagaki, K. Kanjiwara, M. Urukawa, M. Schmidt, Makromol.Chem. 186 (1985) 2623, Table 1 10.1002/macp.1985.021861223 CASWeb of Science®Google Scholar P. Doty, B. Bruce McGill, S.A. Rice, Proc.Natl.Acad.Sci. 44 (1958) 432 (reported by B. Jirgensons, Natural Organic Macromolecules, Pergamon Press, Oxford 1962, p. 309) 10.1073/pnas.44.5.432 CASPubMedWeb of Science®Google Scholar R. Pecora, Science 251 (1992) 893, Table 1 10.1126/science.2000490 PubMedWeb of Science®Google Scholar O.A. Neumüller, Römpps Chemie-Lexikon, Franckh'sche Verlagshandlung, Stuttgart, 8th ed. 1979 Web of Science®Google Scholar S.L. Mayo, B.D. Olafson, W.A. Goddard III , J.Phys.Chem. 94 (1990) 8897, Tables I, III, VII 10.1021/j100389a010 CASWeb of Science®Google Scholar D. Lang, H. Bujard, B. Wolff, D. Russell, J.Mol.Biol. 23 (1967) 163, Plate II 10.1016/S0022-2836(67)80024-X CASPubMedWeb of Science®Google Scholar H.-G. Elias, Grosse Moleküle, Springer-Verlag, Berlin 1985; −, Mega Molecules, Springer-Verlag, Berlin 1987; −, Megamolekulnyi, Leningrad "Khimiya", Leningradskoe Otdelenje 1990, all Figure 14 10.1007/978-3-662-11907-5 Google Scholar G. Natta, P. Corradini, I.W. Bassi, Gazz.Chim.Ital. 89 (1959) 784 CASGoogle Scholar R.L. Jernigan, P.J. Flory, reported by P.J. Flory, Statistical Mechanics of Chain Molecules, Interscience, New York, 1969, p. 147, Fig. 9; P.J. Flory, Science 188 (1975) 1268, Fig. 9 Google Scholar D.H. Yoon, P.J. Flory, Polymer 16 (1975) 645 10.1016/0032-3861(75)90069-5 CASWeb of Science®Google Scholar F. Abe, Y. Einaga, T. Yoshizaki, H. Yamakawa, Macromolecules 26 (1993) 1884, Tables I, II, V 10.1021/ma00060a014 CASWeb of Science®Google Scholar M. Ragnetti, D. Geiser, H. Höcker, R.C. Oberthür, Makromol.Chem. 186 (1985) 1701, Table 1 10.1002/macp.1985.021860819 CASWeb of Science®Google Scholar T. Norisuye, Prog.Polym.Sci. 18 (1993) 543; data of [15]-[16] in Fig. 6 10.1016/0079-6700(93)90017-7 CASWeb of Science®Google Scholar T. Hirao, A. Teramoto, T. Sato, T.Norisuye, T.Masuda, T. Higashimura, Polym.J. 23 (1991) 925, Table 1 10.1295/polymj.23.925 CASWeb of Science®Google Scholar H. Murakami, T. Norisuye, H. Fujita, Macromolecules 13 (1980) 345, Table 1 10.1021/ma60074a026 CASWeb of Science®Google Scholar T. Kashiwagi, T. Norisuye, H. Fujita, Macromolecules 14 (1981) 1220, Table 1 10.1021/ma50006a016 CASWeb of Science®Google Scholar T. Sato, A. Teramoto, Adv.Polym.Sci. 126 (1996) 85 10.1007/3-540-60484-7_3 CASWeb of Science®Google Scholar M.Yamada, M. Osa, T. Yoshizaki, H. Yamakawa, Macromolecules 30 (1997) 7166, Fig. 2 10.1021/ma970738+ CASWeb of Science®Google Scholar Y.Fujii, Y. Tamai, T. Konishi, H. Yamakawa, Macromolecules 24 (1991) 1608, Tables I, II, IV 10.1021/ma00007a025 CASWeb of Science®Google Scholar I. Noda, K. Mizutani, T.Kato, T.Fujimoto, M. Nagasawa, Macromolecules 3 (1970) 787, Table I 10.1021/ma60018a014 Web of Science®Google Scholar Y.Miyaki, Y.Einaga, T. Hirosuye, H. Fujita, Macromolecules 10 (1977) 1356, Tables I, II 10.1021/ma60060a036 CASWeb of Science®Google Scholar N. Hadjichristidis, M. Xenidou, H. Iatrou, M. Pitsikalis, Y. Poulos, A. Avgeropoulos, S.Sioula, S. Paraskeva, G. Velis, D.J. Lohse, D.N. Schulz, L.J. Fetters, P.J. Wright, R.A. Mendelson, C.A. Garcia-Franco, T. Sun, C.J. Ruff, Macromolecules 33 (2000) 2424, Tables 1–8 10.1021/ma991670w CASWeb of Science®Google Scholar S.-T. Sun, I. Nishio, G. Swislow, T. Tanaka, J.Chem.Phys. 73 (1980) 5973, Fig. 2 Google Scholar D. Nerger, M. Eisele, K. Kajiwara, Polym.Bull. 10 (1983) 182, Fig. 1 10.1007/BF00275854 CASWeb of Science®Google Scholar M. Nierlich, J.P. Cotton, B. Farnoux, J.Chem.Phys. 69 (1978) 1379, Table I 10.1063/1.436764 CASWeb of Science®Google Scholar N. Khasat, R.W. Pennisi, H. Hadjichristidis, L.J. Fetters, Macromolecules 21 (1988) 1100, Tables I and II 10.1021/ma00182a042 CASWeb of Science®Google Scholar P.K. Maiti, T. Çağin, G. Wang, W.A. Goddard, III, Macromolecules 37 (2004) 6236 (a) Fig. 5 (b) Table 3 and Figs. 4a and 4b, (c) taken from Fig. 6, (d) Table 2 10.1021/ma035629b CASWeb of Science®Google Scholar T.J. Prosa, B.J. Bauer, E. Amis, Macromolecules 34 (2001) 4897 10.1021/ma0002186 CASWeb of Science®Google Scholar E.J. Amis et al., 29th ACS Central Regional Meeting, Midland (MI), 1997-05-28/30; quoted by P.R. Dvornic, S. Uppuluri, in J.M.J. Fréchet, D.A. Tomalia, Eds., Dendrimers and Other Dendritic Polymers, Wiley, New York 2002 Google Scholar R. Scherrenberg, B. Coussens, P. Van Vliet, G. Eduouard, J. Brackman, E. De Brabander, K. Mortensen, Macromolecules 31 (1998) 456, Table I 10.1021/ma9618181 CASWeb of Science®Google Scholar Macromolecules: Volume 3: Physical Structures and Properties ReferencesRelatedInformation

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