Potential Energy Functions in Conformational Analysis

I get by with a little help from my friends The Beatles: Sgt. Pepper This book should have been in Danish. Any decent person must be able to express himself in his mother's tongue, also when expounding scientific ideas and results. Had I stuck to this ideal, the book would have been read by very few people, and, indeed, appreciated by even fewer. Having it publ­ ished in English gives me a chance to fulfill one ambition: to be read and judged by the international scientific community. Another reason is that the majority of my professional friends are regrettably unread in Danish, just as I am in Hebrew, Finnish and even Italian. I want to deprive them of the most obvious excuse for not reading my opus. Like a man I admired, I will first of all thank my wife. In his autobiography, Meir Weisgal, then President of the Weizmann Insti­ tute of SCience, wrote about his wife: "In addition to her natural endowments - which are considerable - she was a more than competent part-tim~ secretary." He wrote on, and so shall I. The book has been edited by my wife. So if the reader finds the layout pleasant as, in actual fact, I myself do, Birgit is to be praised. If there are blemishes, I am to be blamed for not having caught them.

1 Introduction.- 2 Nomenclature.- 2.1 Crucial expressions.- 2.1.1 Constitution.- 2.1.2 Configuration.- 2.1.3 Conformation.- 2.1.4 Conformer.- 2.1.5 Conformational analysis.- 2.2 Structure.- 2.3 Potential energy function.- 2.3.1 Parameters.- 2.3-2 Potential energy surface.- 2.3.3 Force field.- 2.3.4 Consistent force field.- 2.4 Molecular mechanics.- 3 Potential energy functions: A review.- 3.1 Scope.- 3.2 Plan.- 3.3 Historical background.- 3.4 CFF and variants.- 3.4.1 Lifson and Warshel.- 3.4.2 Warshel.- 3.4.3 Amides.- 3.4.4 Hagler and crystals.- 3.4.5 QCFF/PI.- 3.4.6 Ermer.- 3.4.7 Super-CFF.- 3.5 Karplus.- 3.6 Kollman.- 3.7 Schleyer.- 3.8 Mislow.- 3.9 Bartell.- 3.10 Boyd and variants.- 3.11 Altona and Faber.- 3.12 The Delft group.- 3.13 White.- 3.14 Kitaigorodsky.- 3.15 Allinger.- 3.16 Osawa.- 3.17 Scheraga.- 3.17.1 ECEPP.- 3.17.2 EPEN.- 3.18 Ab initio modelling of non-bonded interactions.- 3.18.1 Function fitting to calculated energies.- 3.18.2 Clementi’s Bond Energy Analysis.- 3.18.3 EPEN going quantum.- 4 Applications: Coordination complexes.- 4.1 An early consistent force field.- 4.2 Australian and American groups.- 4.2.1 Gollogly and Hawkins.- 4.2.2 Sargeson and coworkers.- 4.2.3 Brubaker and coworkers.- 4.2.4 DeHayes and Busch.- 4.3 The Lyngby group.- 4.3.1 Niketic and Woldbye.- 4.3.2 Rasmussen and coworkers.- 4.4 Other groups.- 4.4.1 Pavelcik and Majer.- 4.4.2 McDougall and coworkers.- 4.3.1 Niketic and Woldbye.- 4.3.2 Rasmussen and coworkers.- 4.4.1 Pavelcik and Majer.- 4.4.2 McDougall and coworkers.- 4.4.3 Australians.- 4.4.4 Laier and Larsen.- 4.4.5 Bugnon and Schlaepfer.- 4.4.6 Tapscott and coworkers.- 5 Applications: Saccharides.- 5.1 The glucoses.- 5.2 Maltose.- 5.3 Cellobiose.- 5.4 Gentiobiose.- 5.5 Galactobiose.- 5.6 Misunderstandings.- 6 Applications: Other compounds.- 6.1 Amines.- 6.2 Polynucleotides.- 6.3 Spiro compounds.- 6.4 Chloroalkanes.- 7 Optimisation: Algorithms and implementation.- 7.1 The optimisation algorithm.- 7.2 Termination criteria.- 7.3 The partial derivatives.- 7.3.1 Internal coordinates.- 7.3.2 Rotational constants.- 7.3.3 Atomic charges.- 7.3.4 Dipole moments.- 7-3-5 Internal frequencies.- 7.4 Correlation and uncertainty.- 7.5 Organisation of the optimisation.- 8 A data bank for optimisation.- 8.1 Structure.- 8.1.1 Alkanes.- 8.1.2 Cycloalkanes.- 8.1.3 Ethers.- 8.1.4 Cyclic ethers.- 8.1.5 Alcohols.- 8.1.6 Esters and lactones.- 8.1.7 Amines.- 8.1.8 Chloroalkanes.- 8.2 Vibrational frequency.- 8.3 Fractional atomic charge.- 8.4 Dipole moment.- 8.5 Rotational constants.- 8.6 Unit cell dimensions.- 8.7 Statistical test.- 8.7-1 Alkanes and cycloalkanes.- 8.7.2 Ethers and cyclic ethers.- 8.8 Use of the data.- 9 Potential energy functions: Optimisations.- 9.1 PEF300 series.- 9.1.1 Experimental data.- 9.1.2 Initial experiences.- 9.1.3 Initial results.- 9.1.4 Further results.- 9.2 PEF400 series.- 9.3 Comparisons.- 10 Applications: Alkanes and cycloalkanes.- 10.1 Non-optimised potential energy functions.- 10.2 Optimised potential energy functions.- 10.2.1 Cyclopentane.- 10.2.2 Rotational barriers.- 10.2.3 Rotational constants.- 10.2.4 Hexamethylethane.- 10.2.5 Cyclohexane inversion.- 10.2.6 Cyclodecane..- 10.3 Reliability.- 11 Extension to crystals.- 11.1 Methods.- 11.1.1 Coordinate systems.- 11.1.2 Derivatives.- 11.1.3 Lattice summation.- 11.2 Implementation.- 11.3 Test calculations..- 11.3.1 Argon.- 11.3.2 Ethane.- 11.3.3 Potassium chloride and sodium chloride.- 11.4 Optimisation on crystals.- 11.4.1 Choice of algorithm.- 11.4.2 Derivatives in parameters.- 11.5 Implementation.- 11.6 Test calculations.- 11.6.1 Argon and potassium chloride.- 11.6.2 Alkanes.- 12 Potential energy functions: Recommendations.- 12.1 General guidelines.- 12.2 Packages.- 12.3 Parameter sets.- A1 Availability of the Lyngby CFF program.- A2 User Manual.- A2.1 Summary of the JCL for CFF under IBM MVS.- A2.1.1 Routine operation.- A2.1.2 Program changes.- A2.1.3 Subprogram statistics.- A2.2 Input to the conformational program.- A2.2.1 Cautioning.- A2.3 An example: cyclohexane.- A2.4 A second example: the ethane crystal.- A3 The system of programs.- A3.1 The CFF system.- A3.2 Interfaces.- A3.3 Utilities.- A4 JCL procedure CFF.- A5 TSO command list CFF.- A6 The future of CFF.- Literature references.- Index of names.