Appendix 1: Published Force Field Parameters

Ōsawa, Eiji; Lipkowitz, Kenny B.

doi:10.1002/9780470125830.ch6

Cited by 10 publications

(1 citation statement)

References 423 publications

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“…Published FF parameters for MM (Jalaie and Lipkowitz, 2000;Osawa and Lipkowitz, 1995) and software for molecular modeling (Boyd, 1995) de/spec/sweet2/doc/input/liblist.html, but not all templates have parameters for minimization):…”

Section: Computational Application Of Molecular Modeling Packagesmentioning

confidence: 99%

Phylogenetic Analysis

2002

An Introduction to Computational Biochemistry

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Internet resources) and Chapter 4 (computer graphics). Computational applications in structural biochemistry are described in Chapter 5 (biochemical compounds) and then in Chapters 14 and 15 (molecular modeling). Dynamic biochemistry is treated in Chapter 6 (biomolecular interactions), Chapter 7 (enzyme kinetics), and Chapter 8 (metabolic simulation). Information biochemistry that overlaps bioinformatics and utilizes the Internet resources extensively is discussed in Chapters 9 and 10 (genomics), Chapters 11 and 12 (proteomics), and Chapter 13 (phylogenetic analysis).I would like to thank all the authors who elucidate sequences and 3D structures of nucleic acids as well as proteins, and they kindly place such valuable information in the public domain. The contributions of all the authors who develop algorithms for free access on the Web sites and who provide highly useful software programs for free distribution are gratefully acknowledged. I thank them for granting me the permissions to reproduce their web pages, online and e-mail returns. I am grateful to Drs. Athel Cornish-Bowden (Leonora), Tom Hall (BioEdit), Petr Kuzmic (DynaFit), and Pedro Mendes (Gepasi) for the consents to use their software programs. The effort of all the developers and managers of the many outstanding Web sites are most appreciated. The development of this text would not have been possible without the contribution and generosity of these investigators, authors, and developers. I am thankful to Dr. D. R. Wiles for reading parts of this manuscript. It is my pleasure to state that the writing of this text has been a family effort. My wife, Alice, has been most instrumental in helping me complete this text by introducing and continuously coaching me on the wonderful world of microcomputers. My son, Willis, and my daughter, Ellie, have assisted me in various stages of this endeavor. The credit for the realization of this textbook goes to Luna Han, Editor, and Danielle Lacourciere, Associate Managing Editor, of John Wiley & Sons. This book is dedicated to Alice.

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Section: Computational Application Of Molecular Modeling Packagesmentioning

confidence: 99%

Phylogenetic Analysis

2002

An Introduction to Computational Biochemistry

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Molecular mechanics study of transannular amine-ketone (N?C(DOUBLE BOND)O) interaction in medium-sized heterocycles

Griffith¹,

Bremner²,

Titmuss³

1997

J. Comput. Chem.

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Improved intermolecular force field for crystalline oxohydrocarbons including O?H?O hydrogen bonding

Williams

2000

J. Comput. Chem.

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An improved intermolecular force field of the (exp-6-1) type was obtained by fitting a training set of 124 observed oxohydrocarbon crystal structures and seven observed heats of sublimation. All of these structures, when energy minimized, showed cell edge length shifts of 3% or less. Especially good results were obtained for modeling carbohydrate crystal structures. The fitted crystal structures are a subset of a database of 180 structures systematically selected from the CSD library according to functional group and threshold accuracy criteria. Energy minimization results are also presented for 56 structures not in the training set, which showed cell edge length shifts larger than 3%. The previously published W99 force field, using C(4), C(3), and H(1) potentials, was slightly modified and adopted for hydrocarbon portions of the molecules. Oxygen atoms with one bond, O(1), and those with two bonds, O(2), were assigned separate parameters. Hydrogen atoms bonded to oxygen were assigned exponential repulsion functions and divided into two types: in hydroxy groups, H(2); and in carboxyl groups, H(3). Wavefunctions of HF 6-31g * * quality were calculated for every molecule and the molecular electric potential (MEP) was modeled with net atomic charges. Methylene bisector charges were used for all CH 2 and CH 3 groups, and ring center site charges were added if necessary to fit the MEP. For some structures, upward scaling of the MEP to simulate intermolecular polarization gave better results. MEP interaction generally gave a satisfactory representation of weak C-H. . .O hydrogen bonding. Medium strength C-H. . .O hydrogen bonding was modeled by reducing the repulsion of the involved hydrogen atoms. Crystal structures of several biologically interesting molecules were modeled with the force field, yielding good results. These molecules include aspirin, sucrose, β-cellobiose, β-lactose, progesterone,

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Appendix 1: Published Force Field Parameters

Cited by 10 publications

References 423 publications

Phylogenetic Analysis

Phylogenetic Analysis

Molecular mechanics study of transannular amine-ketone (N?C(DOUBLE BOND)O) interaction in medium-sized heterocycles

Improved intermolecular force field for crystalline oxohydrocarbons including O?H?O hydrogen bonding

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