The Consistent Force Field: A Documentation: 3 - Brossura

Kjeld Rasmussen, Svetozar R. Niketi?

Brossura

ISBN 10: 3540083448 ISBN 13: 9783540083443

Casa editrice: Springer Berlin Heidelberg, 1977

Riassunto

In this chapter ve shall discuss the calculation of potential energy associated vith molecular conforaations. Raving obtained cartesian atoaic coordinates defining conforaations. and lists of intraao- cular interactions, as described in Chapter 3, ve are ready to calculate a quantity which in the chemical literature is known as the total aolecular potential energy or the conforaational, steric, strain or intraaolecular energy. ~he conformational energy of a aolecule can be expressed as a function , of all internal coordinates and interatoaic distances, or as a function of atoaic positions specified by soae general coordi­ Dates. ~he function , is supposed to haye local ainiaa corresponding to the stable equilibrium conforaations of a aolecule in vacuo, Deglecting interaolecular interactions. ~he exact fora of Y is. of course, unknown. We assume that it can be suitably approximated by a sua of different types of energy contri­ hutions: , = Y ., +, +, ., be. nb e ~he teras represent cODtributions to the total aolecular potential energy , due to bond stretching and coapression teras Vb' valence aDgle bending teras 'e' iDterDal rotational or torsional teras V,. DOD-bonded interactions 'nb and electrostatic or Couloab iDter­ actions 'e. If there are other intraaolecular aechanisas affecting 79 V, sucD as hydrogen bonding, corresponding terms say be added.

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Contenuti

Contests.- 1 Introduction.- 1.1 What the CFF is.- 1.2 Background.- 1.3 Pre-CFF.- 1.4 The ascent of CFF.- 1.5 In the wake of CFF.- 2 The Programming System.- 2.1 Introduction.- 2.2 Outline of the programming system.- 2.2.1 Section I.- 2.2.2 Section II.- 2.2.3 Section III.- 2.2.4 Section IV.- 2.2.5 section V.- 2.2.6 Section VI.- 2.2.7 Section VII.- 2.3 Other programmes.- 2.3.1 Utilities.- 2.3.2 CFFPLOT.- 2.3.3 CRYSTAL.- 2.3.4 EDITOR.- 2.3.5 ORTEP.- 2.3.6 MCNSTER.- 2.4 Organisation of the system.- 2.4.1 Overlay structure.- 2.4.2 JCL procedures.- 2.4.2.1 CFFCLIB.- 2.4.2.2 CFFG.- 2.4.2.3 CFFCLG.- 2.4.2.4 CFFECLG.- 2.4.2.5 Listing of CFFECLG.- 2.4.3 Input-output.- 2.5 Input manual.- 3 Molecular Topology and Geometry.- 3.1 Molecular topology.- 3.1.1 Topological representation of chemical structures.- 3.1.2 From structural formula to linear notation.- 3.1.3 Coding of formulae.- 3.1.3.1 Rules for coding line formulae.- 3.1.3.2 Limitations.- 3.1.3.3 Examples.- 3.1.4 Coordination compounds.- 3.1.5 Output from the programmes.- 3.1.5.1 Programme BRACK.- 3.1.5.2 Programme CODER.- 3.2 Lists of interactions.- 3.2.1 Programme MKLIST.- 3.2.2 Interaction codes.- 3.2.3 Coding and decoding of integer words of interaction.- 3.3 Molecular geometry.- 3.3.1 Construction of molecular geometry.- 3.3.2 Coordination compounds.- 3.3.3 Incomplete structures.- 3.3.4 Sideatom positions.- 3.3.5 Torsional angle specification.- 4 The Conformational Energy and its Derivatives.- 4.1 Introduction.- 4.2 Intermolecular forces.- 4.2.1 Non-bonded interactions.- 4.2.2 Electrostatic interactions.- 4.2.3 Hydrogen bonding.- 4.3 Intramolecular forces.- 4.3.1 Bond stretching.- 4.3.2 Bond torsion.- 4.3.3 Angle bending.- 4.3.4 Urey-Bradley potential.- 4.4 Force field parametrisation.- 4.4.1 Parameters and variables.- 4.4.2 Specification of energy functions and parameters.- 4.4.2.1 Global control parameters.- 4.4.2.2 Fonction subroutines.- 4.4.2.3 Energy parameter input.- 4.5 Energy calculations.- 4.5.1 Expansion of V in a Taylor series.- 4.5.2 Energy processing subprogrammes.- 4.5.3 First- and second-order derivative calculation.- 4.5.3.1 Derivatives of interatomic distances.- 4.5.3.2 Derivatives of valence angles.- 4.5.4 Derivatives of torsional angles.- 4.6 Numerical calculation of derivatives.- 5 Energy Minimisation.- 5.1 Statement of the problems.- 5.2 Minimisation algorithms.- 5.2.1 Direct search methods.- 5.2.2 Descent methods.- 5.3 Unified approach to gradient algorithms.- 5.4 Evaluation of minimisation methods.- 5.4.1 The method of steepest descent.- 5.4.2 The Davidon-Fletcher-Powell method.- 5.4.3 The modified Newton method.- 5.5 The minimisation programme.- 5.6 Concluding remarks.- 5.6.1 Minimisation methods in conformational analysis.- 5.6.2 Local versus global minimum.- 5.6.3 False minima.- 6 Vibrational Calculations.- 6.1 The vibrational problem.- 6.2 Normal coordinates.- 6.3 Programme VIBRAT.- 6.4 Practical considerations.- 7 Optimisation of Energy Parameters.- 7.1 The basic algorithm.- 7.2 The partial derivatives.- 7.2.1 Internal coordinates.- 7.2.2 Internal frequencies.- 7.3 Implementation of the optimisation.- 7.3.1 Beading of experimental data.- 7.3.2 Organisation of the optimisation.- 8 Developing A Force Field.- 8.1 The concept of energy functions.- 8.1.1 Bonded interactions.- 8.1.1.1 Bonds.- 8.1.1.2 Torsions.- 8.1.2 Non-bonded interactions.- 8.1.2.1 Atom-atom interactions.- 8.1.2.2 Geminal interactions.- 8.2 Examples.- 8.2.1 Pre-CFF, cyclcalkanes.- 8.2.2 Original CFF, n- and cycloalkanes.- 8.2.3 CFF, alkane crystals.- 8.2.4 CFF, amides and lactams.- 8.2.5 CFF, aaides.- 8.2.6 Flexible amino acids.- 8.2.7 Coordination Compounds.- 8.2.8 Saccharides.- 9 References.

Product Description

Book by Niketic SR Rasmussen K

Dettagli dell'edizione

• Editore: Springer Berlin Heidelberg
• Data di pubblicazione: 1977
• Lingua: Inglese
• ISBN 10: 3540083448
• ISBN 13: 9783540083443
• Rilegatura: Copertina flessibile
• Numero di pagine: 228
• Contatto del produttore: ProductSafety@springernature.com; ProductSafety@springernature.com; ; Poststr. 9; Darmstadt; 64293; Germania