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User Requirements Analysis 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 6. The Locator 150 6.1 Introduction ..............................150 6.2 Objectives ...............................152 6.3 Principles of the Initial Estimate Method ..............153 6.3:1 Rationalisation of the model .................153 6.3.2 Initial Estimate of Hydride Ligand Position ........156 6.4 User Interface .............................166 6.4.1 Output and Experimental Control ..............166 6.4.2 Hydride Ligand Location Procedures ............170 6.5 Performance Evaluation of the Locator ...............173 6.5.1 Models Used ..........................174 6.5.2 Evaluation of the Preliminary Stages of the Locator. 175 6.5.3 Comparative Evaluation the Locator ............179 Table of Contents V 6.5.4 Absolute Evaluation of the Locator .............181 6.5.5 Dihydrogen Models ......................189 6.5.6 HCI Evaluation ........................191 6.6 Conclusions ..............................195 6.7 Further Work ..............................196 6.7.1 Efficiency ............................196 6.7.2 Charge Iteration ........................197 6.7.3 Tuning of the orbital energy and exponent of the metal- bound hydride ligand(s) ...................199 6.7.4 Dihydrogen Models ......................204 6.7.5 The Failure of the Locator for Some Models ........204 7. Conclusions and Further Work 205 7.1 Conclusions ..............................205 7.2 Future Work ..............................209 7.2.1 Improvements to Current Tools ...............209 7.2.2 A Construction Tool ......................210 7.2.3 Future Developments to the Tool-Kit ............211 7.2.4 Broadening the Scope of Applications ...........212 Questionnaire 213 Questionnaire Results 223 B.1 Section 1 -Working practices ....................223 B.2 Section 2 -Library System ......................228 B.3 Section 3 -Use of EMAS .......................229 B.4 Section 4 -User Suggestions ....................231 B.4.1 Library System ........................231 B.4.2 Applications ..........................231 Table of Contents vi B.4.3 User Interface Issues .....................233 B.4.4 Support .............................233 List of Molecular Models 234 Molecular Models 244 The Locator: Raw Results 255 F Comparison of Initial Estimate Methods 262 G. Publications 265 Chapter 1 Introduction Research chemists are finding increasing benefits from the use of computers; the rapid decrease in the cost of computer hardware, allied with ongoing im- provements in quality, has meant that computers and associated software are becoming more and more evident in chemistry. High quality workstations with bit-mapped screens and cheaper, better graphics are gradually taking over from teletype terminals connected to main-frames, enabling more sophisticated and user-friendly software to be run. Corresponding to this rise in quality
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