Effective Software Support for Chemical Research
Amanda Jayne Welsh
Ph.D. University of Edinburgh 1993
(.) for "me mam" Abstract
Locating metal-bound hydride ligands in transition metal cluster compounds can be difficult with conventional analytical chemistry. Thus many empirical and theoretical methods have been developed for locating such ligands. One such method has been implemented in the Complete Coordinate Convergence Program (CCCP). However, on close examination, this tool is found to be user-unfriendly and its success is shown to be dependent on an initial location estimate from the user. Thus the Locator was developed as a tool designed to overcome these problems. Methods are presented which exploit known chemical and spatial restraints in finding an initial estimate of the hydride ligand position(s) for more reliable subsequent optimisation by the CCCP code. The performance of Locator was tested on 178 models, with a favourable success rate of 72%. This figure rises to 84% when taking account of bonding interactions of the hydride ligand(s) provided from the user. These improvements to CCCP were motivated by a user requirements analysis undertaken to identify computational chemistry applications which would benefit from the exploitation of software engineering and HCI principles becoming prevalent in mainstream computer science. A molecular graphics tool was also selected because it was considered that this would be useful to many researchers, and because the available molecular graphics tools were observed to be lacking in terms of human- computer interaction principles. Further, such a tool could be used as a base for other applications. This thesis by no means suggests that the scope of physical scientific applications which would benefit from the uptake of such ideas is limited to this relatively narrow field of chemistry. Rather these tools are considered in a proof of concept case study within the time constraints of this work. The adoption of the Visualisor interface and the addition of the initial estimate routine are considered to have significantly improved hydride ligand location in transition metal clusters both in terms of success and accuracy of the results and the ease with which these results may be obtained. Further, it is considered that this project has demonstrated the benefits of the application of current computer science software development principles to scientific software. Table of Contents
Introduction 1
1.1 Potential Benefits of Computer Software to Chemistry ...... 2
1.2 Barriers to a Wider Use of Computers in Chemistry ...... 4
1.2.1 The Barriers Encountered ...... 4
1.2.2 Causes of the Barriers ...... 6
1.3 Proposed Solution ...... 8
1.3.1 Objectives ...... 8
1.3.2 Method ...... 9
1.3.3 Overview ...... 10
User Requirements Analysis 13
2.1 Introduction ...... 13
2.2 Overview ...... 15
2.2.1 User Resistance ...... 15
2.3 Questionnaire ...... 19
2.3.1 Aims ...... 20
2.4 Results ...... 22
2.4.1 Statistical Analysis of Responses ...... 22
2.4.2 Section 1 -Working Practices ...... 23
1 Table of Contents 11
2.4.3 Section 2— Library System ...... 27
2.4.4 Section 3 -Current Facilities ...... 28
2.5 Discussion ...... 36
2.5.1 Limitations of the Questionnaire ...... 36
2.5.2 Tool Support for User Activities ...... 40
2.5.3 Support Relative to Origin of Software ...... 47
2.6 Conclusions ...... 50
2.6.1 Current State ...... 50
2.6.2 Choice of tools to be implemented ...... 51
2.6.3 Requirements ...... 52
2.6.4 User Model ...... 53
3. Design of the Tool Kit 58
3.1 Introduction ...... 58
3.2 Overview ...... 59
3.2.1 General Issues for Effective Design ...... 59
3.2.2 Software Engineering Issues for Effective Internal Design 61
3.2.3 Human-Computer Interaction Issues for Effective External Design ...... 65
3.3 Objectives ...... 71
3.4 The Tool-Kit ...... 74
3.4.1 The Orthogonalisor ...... 75
3.4.2 The Visualisor ...... 77
3.4.3 The Locator ...... 77
3.5 Implementation ...... 78
3.5.1 General Issues ...... 78
3.5.2 Software Engineering Issues ...... 78 Table of Contents 111
3.5.3 HCI Issues ...... 83
The Visualisor 89
4.1 Introduction ...... 89
4.2 Literature Review ...... 90
4.2.1 Scientific Visualisation ...... 90
4.2.2 Molecular Graphics ...... 92
4.3 Objectives ...... 96
4.4 Implementation ...... 97
4.4.1 Files Menu ...... 99
4.4.2 View Menu ...... 101
4.4.3 Print Menu ...... 102
4.4.4 Display Menu ...... 104
4.4.5 Chemical Knowledge ...... 104
4.5 Evaluation ...... 105
4.5.1 Achievement of Objectives ...... 106
4.6 Discussion ...... 111
4.7 Conclusions ...... 112
4.8 Further Work ...... 113
4.8.1 Atom Number Restrictions ...... 113
4.8.2 Loading and Saving Files ...... 113
4.8.3 Display ...... 114
4.8.4 PostScript Output ...... 116
4.8.5 Keyboard Shortcuts ...... 116
Hydride Ligand Location in Transition Metal Complexes 118
5.1 Introduction ...... 118
5.1.1 Characterisation ...... 118
Table of Contents lv
5.1.2 X-ray Diffraction ...... 119
5.1.3 Neutron Diffraction ...... 120
5.2 Current Methods of Hydride Ligand Location ...... 121
5.2.1 Steric Methods ...... 121
5.2.2 Potential Energy Calculations ...... 122
5.2.3 Molecular Orbital Calculations ...... 125
5.3 Analysis of CCCP ...... 131
5.3.1 Stage 1: Failure of CCCP ...... 135
5.3.2 Stage 2: Investigation of the area around the known "correct" position ...... 137
5.3.3 Stage 3: Estimates using Chemical Knowledge ...... 140
5.3.4 User Interface ...... 143
5.4 Conclusions ...... 148