Appendix A Appendix A ? MM Data General Methodology to Calculate Charges Before starting MM calculations, the atoms in the molecule had to be assigned charges. In the Setup menu Semi-empirical was selected. Under the Options tab, the total charge was set to 0, the charge of the free ligand. The spin multiplicity was set to zero. The Restricted Hartree-Fock method (RHF) was selected for spin pairing. The lowest state was selected and the convergence limit was set to 0.0001 kcal mol-1 or an iteration limit of 500 was selected in the SCF Controls section. The convergence was accelerated. Once all of these parameters had been set, a single point calculation was performed by selecting Single Point from the Compute menu. The resultant molecule was saved. To view to charges on each molecule, Labels was selected from the Display menu. In the dialog box, Charges was selected for Atom. General Methodology to Perform MM Calculations In order for the MM calculations to be performed, one had to set the MM settings in HyperChem. This was done by selecting the Setup Menu and selecting the AMBER option. In the adjoining Options tab, the dielectric constant, K, was set to 76 (the dielectric constant of water), and both the Electrostatic and van der Waals 1-4 scale factors were set to 0.5. These two scaling factors set the scaling of the nonbonded interactions of the atoms that are separated by three atoms. This is the default setting for AMBER. This ensures that the energy is not dominated by van der Waals and electrostatic terms but rather by bond lengths and angles. Under the Cutoffs tab, None was selected. The tabs were then closed. Form the Setup menu, Select Parameter Set was selected. In the window that opened WitsGAFF was selected and the window closed. From the Setup menu, Compile Parameter Set was then selected. Once all of these parameters had been set, the atom types for each of the atoms in the molecule were selected according to the specifications given by Kollman and his 1 Appendix A colleagues.6 This was done by selecting Atom Type in the Build menu. Once all atom types had been assigned, one could view the types by selecting Labels from the Display menu. In the dialog box, Type was selected for Atom. Once the desired dielectric constant had been set, the molecule was submitted for a MM geometry optimisation. Under the Compute menu Geometry Optimization was selected. The algorithm used was the Polak-Ribiere (Conjugate gradient). The system was set to be in vacuo, and the termination conditions were set to a root-mean-square, RMS, gradient of less than 0.001 kcal/(? mol) or at least 5000 cycles. This large number of cycles ensured that the first termination condition was reached first. The window was then closed by selecting OK. This started the calculation. General Methodology to Perform Simulated Annealing This method added energy to the system in the form of heat so that the different energy barriers between the different structural isomers could be overcome. This was done by setting the parameters for the simulated annealing in the molecular dynamics menu. This was to be found under Compute. The simulated annealing process was built up in the following manner: the simulation started at a temperature of 0 K and was heated to 800 K over 10 ps. The molecule was then kept at a constant temperature of 800 K for different run times of between 5 and 100 ps, in 5 ps intervals. The molecule was then cooled to 0 K over a period of 20 ps. The step size was set as 1 fs or 0.001 ps. The resulting structures were then saved and MM calculations performed to find the total energy of the molecule. Cy2-en Data Table A.1: Cy2-en Data After Simulated Annealing C-C C-N C-O C-C-C C-C-N C-C-O C-N-C XRD Cy2-en_002 Average 1.518 1.475 1.427 111.1 110.6 109.8 113.7 Std Dev 0.006 0.002 0.000 0.7 1.4 0.9 0.0 MM w ZINDO1 Cy2-en_004 2 Appendix A e = 76 Average 1.545 1.480 1.432 111.2 110.2 109.3 114.5 Std Dev 0.005 0.004 0.000 0.4 1.2 0.4 0.0 Annealing Cy2-en_010 run time = 10 ps Average 1.546 1.481 1.432 111.2 110.3 109.4 115.5 Std Dev 0.006 0.003 0.002 0.6 2.1 1.5 1.4 Annealing Cy2-en_011 run time = 20 ps Average 1.548 1.484 1.431 111.7 111.2 109.1 117.6 Std Dev 0.007 0.005 0.000 0.9 2.8 1.7 1.3 Annealing Cy2-en_012 run time = 30 ps Average 1.547 1.479 1.432 111.6 110.2 109.1 114.7 Std Dev 0.006 0.003 0.001 0.8 1.3 0.4 0.2 Annealing Cy2-en_013 run time = 40 ps Average 1.546 1.480 1.432 111.4 110.2 109.4 114.8 Std Dev 0.005 0.004 0.000 0.5 1.4 0.8 0.1 Annealing Cy2-en_014 run time = 50 ps Average 1.547 1.480 1.432 111.6 110.5 109.5 114.5 Std Dev 0.005 0.002 0.000 1.0 0.8 0.5 0.5 Annealing Cy2-en_015 run time = 60 ps Average 1.545 1.482 1.432 111.2 110.6 109.3 115.7 Std Dev 0.004 0.004 0.000 0.4 1.5 0.4 1.7 Annealing Cy2-en_016 run time = 70 ps Average 1.546 1.480 1.431 111.2 110.2 109.5 115.7 Std Dev 0.006 0.003 0.002 0.5 2.0 1.5 1.2 Annealing Cy2-en_017 run time = 80 ps Average 1.548 1.482 1.432 111.8 110.7 109.4 115.6 Std Dev 0.005 0.003 0.000 0.8 1.5 0.4 1.1 Annealing Cy2-en_018 run time = 90 ps Average 1.545 1.482 1.432 111.1 111.0 109.4 115.7 Std Dev 0.004 0.003 0.001 0.3 1.2 0.8 1.1 Annealing Cy2-en_019 3 Appendix A run time = 100 ps Average 1.545 1.482 1.432 111.2 110.7 109.2 115.4 Std Dev 0.004 0.003 0.000 0.3 1.6 0.3 1.6 Annealing Cy2-en_020 run time = 5 ps Average 1.545 1.480 1.432 111.2 110.0 109.4 115.5 Std Dev 0.006 0.004 0.002 0.6 2.1 1.5 1.4 Annealing Cy2-en_021 run time = 15 ps Average 1.546 1.484 1.432 111.1 111.3 109.6 116.6 Std Dev 0.004 0.004 0.001 0.4 1.6 0.5 0.3 Annealing Cy2-en_022 run time = 25 ps Average 1.545 1.482 1.432 111.1 111.0 109.4 115.8 Std Dev 0.005 0.003 0.000 0.3 1.3 0.7 1.2 Annealing Cy2-en_023 run time = 35 ps Average 1.546 1.482 1.432 111.3 110.9 109.6 115.7 Std Dev 0.005 0.005 0.001 0.5 1.8 0.3 1.3 Annealing Cy2-en_024 run time = 45 ps Average 1.547 1.482 1.432 111.3 111.1 109.6 115.7 Std Dev 0.005 0.003 0.000 0.5 1.7 0.7 1.3 Annealing Cy2-en_025 run time = 55 ps Average 1.545 1.482 1.432 111.1 110.8 109.6 115.5 Std Dev 0.005 0.004 0.000 0.4 1.5 0.6 1.4 Annealing Cy2-en_026 run time = 65 ps Average 1.546 1.480 1.432 111.4 110.4 109.4 114.9 Std Dev 0.005 0.002 0.000 0.5 1.2 0.3 0.1 Annealing Cy2-en_027 run time = 75 ps Average 1.547 1.480 1.432 111.6 110.4 109.7 115.2 Std Dev 0.005 0.003 0.000 0.5 1.6 0.2 0.0 Annealing Cy2-en_028 run time = 85 ps Average 1.546 1.481 1.432 111.4 110.4 109.4 114.9 Std Dev 0.005 0.002 0.000 0.5 1.3 0.4 0.2 Annealing Cy2-en_029 4 Appendix A run time = 95 ps Average 1.548 1.483 1.432 111.7 110.8 109.2 116.6 Std Dev 0.007 0.005 0.002 0.9 2.9 1.6 2.5 Comparisons 002 - 004 Average 0.027 0.005 0.004 0.0 0.4 0.5 0.8 Std Dev 0.001 0.002 0.000 0.3 0.2 0.4 0.0 Comparisons 002 - 010 Average 0.028 0.006 0.004 0.1 0.3 0.4 1.8 Std Dev 0.000 0.001 0.002 0.2 0.7 0.6 1.4 Comparisons 002 - 011 Average 0.030 0.009 0.004 0.5 0.6 0.8 3.9 Std Dev 0.001 0.003 0.000 0.2 1.4 0.9 1.3 Comparisons 002 - 012 Average 0.029 0.005 0.005 0.5 0.4 0.7 1.0 Std Dev 0.001 0.002 0.000 0.1 0.1 0.5 0.1 Comparisons 002 - 013 Average 0.028 0.005 0.005 0.3 0.3 0.4 1.0 Std Dev 0.000 0.002 0.000 0.2 0.1 0.1 0.1 Comparisons 002 - 014 Average 0.029 0.005 0.005 0.5 0.1 0.3 0.8 Std Dev 0.000 0.001 0.000 0.2 0.7 0.3 0.5 Comparisons 002 - 015 Average 0.027 0.007 0.004 0.0 0.0 0.5 2.0 Std Dev 0.001 0.002 0.000 0.3 0.1 0.4 1.7 Comparisons 002 - 016 Average 0.028 0.006 0.004 0.1 0.3 0.3 2.0 Std Dev 0.000 0.001 0.002 0.2 0.6 0.6 1.1 Comparisons 002 - 017 Average 0.030 0.007 0.005 0.6 0.1 0.4 1.9 Std Dev 0.000 0.002 0.000 0.1 0.1 0.5 1.1 Comparisons 002 - 018 Average 0.028 0.007 0.004 0.1 0.4 0.4 2.0 Std Dev 0.001 0.002 0.000 0.4 0.2 0.1 1.1 Comparisons 002 - 019 Average 0.027 0.007 0.005 0.1 0.2 0.6 1.7 Std Dev 0.002 0.002 0.000 0.4 0.1 0.5 1.6 Comparisons 002 - 020 Average 0.027 0.005 0.004 0.1 0.6 0.4 1.8 5 Appendix A Std Dev 0.000 0.002 0.002 0.2 0.7 0.6 1.4 Comparisons 002 - 021 Average 0.028 0.009 0.005 0.0 0.7 0.2 2.9 Std Dev 0.002 0.002 0.001 0.3 0.1 0.3 0.3 Comparisons 002 - 022 Average 0.028 0.007 0.004 0.0 0.4 0.4 2.0 Std Dev 0.001 0.002 0.000 0.4 0.1 0.1 1.2 Comparisons 002 - 023 Average 0.029 0.007 0.004 0.2 0.3 0.2 2.0 Std Dev 0.001 0.003 0.001 0.2 0.4 0.6 1.2 Comparisons 002 - 024 Average 0.029 0.007 0.005 0.2 0.5 0.2 2.0 Std Dev 0.001 0.002 0.000 0.2 0.3 0.2 1.2 Comparisons 002 - 025 Average 0.028 0.007 0.005 0.0 0.2 0.2 1.8 Std Dev 0.001 0.003 0.000 0.4 0.1 0.3 1.3 Comparisons 002 - 026 Average 0.028 0.005 0.005 0.3 0.2 0.4 1.2 Std Dev 0.001 0.001 0.000 0.2 0.3 0.5 0.0 Comparisons 002 - 027 Average 0.029 0.005 0.005 0.5 0.2 0.1 1.5 Std Dev 0.001 0.001 0.000 0.2 0.2 0.6 0.0 Comparisons 002 - 028 Average 0.028 0.006 0.005 0.3 0.2 0.4 1.2 Std Dev 0.001 0.001 0.000 0.2 0.1 0.5 0.2 Comparisons 002 - 029 Average 0.030 0.008 0.005 0.6 0.2 0.6 2.9 Std Dev 0.001 0.003 0.002 0.2 1.4 0.8 2.5 Cy2-Otn Data Table A.2: Charges on Cy2-Otn Calculated by Semi-empirical Methods Using PM3 and ZINDO/1 Atom PM3 charge ZINDO/1 charge Secondary amine nitrogen, NH -0.019 -0.324 Secondary amine nitrogen, NH -0.008 -0.319 Alcohol group on ring, OH -0.305 -0.398 Alcohol group on ring, OH -0.309 -0.403 Alcohol group on propylene bridge, OH -0.313 -0.397 Carbon on propylene bridge bonded to amine, CH2 -0.122 -0.008 6 Appendix A 7 Carbon on propylene bridge bonded to amine, CH2 -0.096 0.004 Carbon on ring bonded to amine, CH -0.109 0.076 Carbon on ring bonded to amine, CH -0.106 0.074 Carbon on ring bonded to alcohol, CH 0.079 0.152 Carbon on ring bonded to alcohol, CH 0.073 0.145 Carbon on propylene bridge boned to alcohol, OH 0.075 0.144 Table A.3: Energies of Cy2-Otn after Simulated Annealing Runs with Various Run Times Compared to the Energy of the XRD Structure Run Time Energy [kcal/mol] XRD structure 19.563 5 ps 19.257 10 ps 25.740 15 ps 18.620 20 ps 19.735 25 ps 18.951 30 ps 18.763 35 ps 20.588 40 ps 20.141 45 ps 22.103 50 ps 20.107 55 ps 18.592 60 ps 30.107 65 ps 18.001 70 ps 18.816 75 ps 18.319 80 ps 24.677 85 ps 18.463 90 ps 18.213 95 ps 24.722 100 ps 20.332 Appendix A Table A.4: Cy2-Otn Data After Simulated Annealing C-C C-N C-O C-C-C C-C-O C-C-N C-N-C XRD Cy2Otn_001 Average 1.513 1.463 1.425 111.0 110.6 110.7 113.4 Std Dev 0.007 0.007 0.005 0.8 1.6 1.1 1.7 ZINDO/1 geom Cy2Otn_004 Average 1.545 1.481 1.433 111.1 109.5 110.6 114.6 Std Dev 0.005 0.003 0.000 0.6 0.9 1.1 0.2 Annealing Cy2Otn_005 Run time = 5 ps Average 1.546 1.480 1.431 111.3 109.1 110.5 115.1 Std Dev 0.004 0.002 0.002 0.6 0.9 1.2 0.1 Annealing Cy2Otn_006 Run time = 10 ps Average 1.548 1.481 1.430 111.8 109.1 110.5 115.1 Std Dev 0.007 0.002 0.000 1.0 1.2 2.4 0.3 Annealing Cy2Otn_007 Run time = 15 ps Average 1.545 1.481 1.432 111.2 109.5 110.6 114.7 Std Dev 0.004 0.002 0.001 0.4 0.6 1.2 0.3 Annealing Cy2Otn_008 Run time = 20 ps Average 1.546 1.482 1.431 111.1 109.3 111.0 115.7 Std Dev 0.004 0.004 0.001 0.3 0.7 1.2 1.0 Annealing Cy2Otn_009 Run time = 25 ps Average 1.545 1.480 1.433 111.1 109.6 110.4 114.8 Std Dev 0.004 0.002 0.000 0.5 0.5 1.0 0.0 Annealing Cy2Otn_010 Run time = 30 ps Average 1.545 1.480 1.432 111.2 109.3 110.4 114.9 Std Dev 0.004 0.002 0.001 0.4 0.5 1.0 0.0 Annealing Cy2Otn_011 Run time = 35 ps Average 1.546 1.482 1.433 111.3 110.0 111.8 115.8 Std Dev 0.004 0.002 0.001 0.6 1.3 1.5 1.4 8 Appendix A Annealing Cy2Otn_012 Run time = 40 ps Average 1.546 1.483 1.432 111.1 109.5 111.3 115.6 Std Dev 0.004 0.003 0.001 0.4 0.8 1.1 1.2 Annealing Cy2Otn_013 Run time = 45 ps Average 1.546 1.482 1.431 111.1 109.5 111.0 116.5 Std Dev 0.005 0.004 0.001 0.5 1.4 2.2 0.0 Annealing Cy2Otn_014 Run time = 50 ps Average 1.546 1.482 1.432 111.1 109.7 111.2 115.7 Std Dev 0.004 0.003 0.000 0.3 0.5 1.3 1.3 Annealing Cy2Otn_015 Run time = 55 ps Average 1.546 1.480 1.432 111.4 109.3 110.4 114.8 Std Dev 0.004 0.003 0.001 0.5 0.4 1.4 0.5 Annealing Cy2Otn_016 Run time = 60 ps Average 1.549 1.480 1.432 112.2 109.0 110.5 115.0 Std Dev 0.006 0.002 0.001 0.8 0.6 1.7 0.3 Annealing Cy2Otn_017 Run time = 65 ps Average 1.547 1.482 1.432 111.5 109.9 111.2 114.7 Std Dev 0.004 0.002 0.001 0.7 0.7 1.7 0.1 Annealing Cy2Otn_018 Run time = 70 ps Average 1.546 1.480 1.431 111.3 109.0 110.5 115.1 Std Dev 0.004 0.002 0.001 0.5 0.8 1.2 0.1 Annealing Cy2Otn_019 Run time = 75 ps Average 1.545 1.480 1.431 111.2 109.2 110.4 114.9 Std Dev 0.004 0.002 0.000 0.4 0.4 1.0 0.1 Annealing Cy2Otn_020 Run time = 80 ps Average 1.547 1.480 1.432 111.6 109.3 110.5 114.9 Std Dev 0.005 0.002 0.001 0.9 0.4 1.3 0.0 Annealing Cy2Otn_021 Run time = 85 ps Average 1.546 1.480 1.432 111.3 109.4 110.5 114.6 Std Dev 0.004 0.001 0.001 0.5 0.4 1.2 0.4 9 Appendix A Annealing Cy2Otn_022 Run time = 90 ps Average 1.545 1.480 1.432 111.1 109.4 110.4 114.7 Std Dev 0.004 0.003 0.001 0.5 0.4 1.1 0.2 Annealing Cy2Otn_023 Run time = 95 ps Average 1.547 1.482 1.432 111.6 109.2 110.8 115.9 Std Dev 0.005 0.003 0.001 0.8 0.5 1.9 1.1 Annealing Cy2Otn_024 Run time = 100 ps Average 1.547 1.482 1.432 111.3 109.5 111.1 115.7 Std Dev 0.004 0.004 0.000 0.5 0.7 1.4 1.1 Comparisons 001 - 004 Average 0.032 0.019 0.008 0.0 1.1 0.1 1.2 Std Dev 0.002 0.004 0.004 0.2 0.8 0.0 1.5 Comparisons 001 - 005 Average 0.032 0.017 0.007 0.2 1.5 0.2 1.7 Std Dev 0.002 0.005 0.003 0.3 0.7 0.1 1.6 Comparisons 001 - 006 Average 0.035 0.018 0.006 0.7 1.5 0.2 1.7 Std Dev 0.000 0.005 0.005 0.2 0.5 1.3 1.4 Comparisons 001 - 007 Average 0.032 0.018 0.008 0.1 1.1 0.1 1.3 Std Dev 0.003 0.005 0.004 0.5 1.0 0.2 1.4 Comparisons 001 - 008 Average 0.032 0.019 0.007 0.1 1.3 0.3 2.3 Std Dev 0.003 0.003 0.004 0.5 1.0 0.1 0.6 Comparisons 001 - 009 Average 0.032 0.017 0.008 0.1 1.0 0.3 1.4 Std Dev 0.003 0.004 0.005 0.3 1.1 0.1 1.7 Comparisons 001 - 010 Average 0.032 0.017 0.007 0.1 1.3 0.3 1.5 Std Dev 0.003 0.004 0.004 0.4 1.1 0.1 1.6 Comparisons 001 - 011 Average 0.033 0.000 0.000 2.0 1.0 4.3 0.0 Std Dev 0.002 0.000 0.000 0.1 0.0 0.0 0.0 Comparisons 001 - 012 Average 0.032 0.020 0.007 0.0 1.1 0.6 2.2 Std Dev 0.002 0.004 0.004 0.4 0.9 0.1 0.5 10 Appendix A Comparisons 001 - 013 Average 0.032 0.020 0.007 0.1 1.1 0.3 3.1 Std Dev 0.002 0.003 0.004 0.3 0.3 1.1 1.7 Comparisons 001 - 014 Average 0.032 0.020 0.008 0.1 0.9 0.5 2.3 Std Dev 0.003 0.003 0.004 0.5 1.1 0.2 0.4 Comparisons 001 - 015 Average 0.033 0.018 0.007 0.3 1.3 0.3 1.4 Std Dev 0.002 0.004 0.004 0.3 1.2 0.4 1.2 Comparisons 001 - 016 Average 0.035 0.017 0.007 1.2 1.6 0.2 1.6 Std Dev 0.001 0.005 0.004 0.1 1.0 0.7 1.4 Comparisons 001 - 017 Average 0.033 0.019 0.007 0.5 0.7 0.5 1.3 Std Dev 0.002 0.005 0.004 0.2 0.9 0.6 1.6 Comparisons 001 - 018 Average 0.032 0.017 0.006 0.2 1.6 0.2 1.7 Std Dev 0.003 0.005 0.003 0.3 0.8 0.1 1.6 Comparisons 001 - 019 Average 0.032 0.017 0.007 0.1 1.4 0.3 1.5 Std Dev 0.003 0.004 0.004 0.5 1.3 0.1 1.6 Comparisons 001 - 020 Average 0.033 0.017 0.007 0.6 1.3 0.3 1.5 Std Dev 0.002 0.005 0.004 0.1 1.2 0.2 1.7 Comparisons 001 - 021 Average 0.032 0.017 0.007 0.2 1.2 0.2 1.2 Std Dev 0.003 0.005 0.004 0.3 1.2 0.1 1.3 Comparisons 001 - 022 Average 0.032 0.018 0.008 0.0 1.2 0.3 1.3 Std Dev 0.003 0.004 0.004 0.3 1.3 0.0 1.4 Comparisons 001 - 023 Average 0.034 0.019 0.007 0.5 1.5 0.1 2.5 Std Dev 0.001 0.003 0.004 0.0 1.1 0.8 0.6 Comparisons 001 - 024 Average 0.033 0.000 0.001 0.1 0.0 0.1 0.1 Std Dev 0.000 0.000 0.002 0.1 0.8 0.2 1.6 11 Appendix A BHEEN Data Table A.5: Charges on BHEEN Calculated by Semi-empirical Methods Using PM3 and ZINDO/1 Atom PM3 charge ZINDO/1 charge Secondary amine nitrogen, NH 0.844 -0.016 Secondary amine nitrogen, NH 0.788 -0.028 Alcohol group, OH -0.294 -0.364 Alcohol group, OH -0.274 -0.352 Carbon on ethylene bridge bonded to both amines, CH2 -0.247 -0.012 Carbon on ethylene bridge bonded to both amines, CH2 -0.212 -0.000 Carbon on ethylene bridge between alcohol and amine, bonded to amine, CH2 -0.244 -0.014 Carbon on ethylene bridge between alcohol and amine, bonded to amine, CH2 -0.240 -0.012 Carbon bonded to alcohol, CH2 0.084 0.081 Carbon bonded to alcohol, CH2 0.087 0.083 Table A.6: Energies of BHEEN after Simulated Annealing Runs with Various Run Times Compared to the Energy of the XRD Structure Run Time Energy [kcal/mol] XRD structure 5 ps 2.798 10 ps 2.334 15 ps 1.772 20 ps 1.007 25 ps 4.595 30 ps 4.380 35 ps 1.614 40 ps 1.716 45 ps 2.153 50 ps 2.531 55 ps 1.160 60 ps 1.007 65 ps 2.220 70 ps 1.805 75 ps 2.216 80 ps 2.254 85 ps 2.073 90 ps 2.271 95 ps 1.881 100 ps 2.066 12 Appendix A Table A.7: BHEEN Data After Simulated Annealing C-C C-N C-O C-C-N C-C-O C-N-C XRD bheen_001 Average 1.511 1.486 1.415 109.654 109.639 112.726 Std Dev 0.005 0.004 0.000 0.252 0.000 0.000 Annealing bheen_006 run time = 5 ps Average 1.542 1.514 1.429 110.978 110.276 112.994 Std Dev 0.004 0.001 0.001 1.222 0.239 0.001 Annealing bheen_007 run time = 10 ps Average 1.540 1.512 1.428 110.283 109.904 112.234 Std Dev 0.002 0.003 0.001 1.213 0.371 1.052 Annealing bheen_008 run time = 15 ps Average 1.540 1.512 1.428 110.295 109.697 112.263 Std Dev 0.003 0.002 0.001 1.227 0.565 1.058 Annealing bheen_009 run time = 20 ps Average 1.538 1.509 1.428 109.427 109.700 111.472 Std Dev 0.001 0.001 0.001 0.422 0.559 0.015 Annealing bheen_010 run time = 25 ps Average 1.543 1.517 1.428 111.590 109.856 115.015 Std Dev 0.001 0.001 0.001 0.515 0.515 0.019 Annealing bheen_011 run time = 30 ps Average 1.541 1.514 1.428 110.698 109.566 113.998 Std Dev 0.003 0.003 0.000 1.087 0.103 1.385 Annealing bheen_012 run time = 35 ps Average 1.540 1.512 1.429 110.401 110.128 112.280 Std Dev 0.002 0.002 0.000 1.031 0.061 1.027 Annealing bheen_013 run time = 40 ps Average 1.540 1.512 1.428 110.279 109.682 112.282 Std Dev 0.003 0.002 0.001 1.228 0.543 1.056 13 Appendix A Annealing bheen_014 run time = 45 ps Average 1.539 1.511 1.429 109.835 109.865 112.196 Std Dev 0.002 0.002 0.002 0.940 0.800 1.019 Annealing bheen_015 run time = 50 ps Average 1.540 1.512 1.429 110.336 109.950 112.215 Std Dev 0.001 0.001 0.002 0.563 1.076 1.067 Annealing bheen_016 run time = 55 ps Average 1.539 1.510 1.428 109.808 109.701 111.509 Std Dev 0.001 0.001 0.001 0.401 0.560 0.019 Annealing bheen_017 run time = 60 ps Average 1.538 1.509 1.428 109.428 109.698 111.471 Std Dev 0.001 0.001 0.001 0.422 0.558 0.014 Annealing bheen_018 run time = 65 ps Average 1.540 1.512 1.428 110.293 109.866 112.262 Std Dev 0.002 0.002 0.001 1.230 0.326 1.058 Annealing bheen_019 run time = 70 ps Average 1.540 1.512 1.428 110.297 109.706 112.255 Std Dev 0.003 0.003 0.001 1.191 0.569 1.080 Annealing bheen_020 run time = 75 ps Average 1.540 1.512 1.428 110.291 109.866 112.263 Std Dev 0.002 0.002 0.001 1.228 0.326 1.055 Annealing bheen_021 run time = 80 ps Average 1.540 1.512 1.428 110.295 109.874 112.255 Std Dev 0.002 0.003 0.001 1.193 0.331 1.081 Annealing bheen_022 run time = 85 ps Average 1.542 1.514 1.429 110.889 110.165 113.082 Std Dev 0.002 0.001 0.000 1.148 0.077 0.053 Annealing bheen_023 run time = 90 ps Average 1.541 1.514 1.429 110.844 110.168 113.002 Std Dev 0.003 0.001 0.000 1.276 0.000 0.000 14 Appendix A Annealing bheen_024 run time = 95 ps Average 1.538 1.510 1.427 109.660 109.246 112.201 Std Dev 0.002 0.002 0.000 0.967 0.082 1.045 Annealing bheen_025 run time = 100 ps Average 1.540 1.511 1.429 110.043 110.268 112.202 Std Dev 0.000 0.002 0.001 0.810 0.231 1.027 Comparisons 001 - 006 Average 0.031 0.028 0.014 1.323 0.636 0.269 Std Dev 0.001 0.003 0.001 0.970 0.239 0.001 Comparisons 001 - 007 Average 0.029 0.026 0.013 0.629 0.265 0.492 Std Dev 0.002 0.001 0.001 0.961 0.371 1.052 Comparisons 001 - 008 Average 0.029 0.026 0.013 0.641 0.058 0.462 Std Dev 0.002 0.001 0.001 0.975 0.565 1.058 Comparisons 001 - 009 Average 0.027 0.023 0.013 0.227 0.061 1.254 Std Dev 0.004 0.003 0.001 0.170 0.559 0.015 Comparisons 001 - 010 Average 0.032 0.031 0.013 1.935 0.216 2.289 Std Dev 0.004 0.003 0.001 0.262 0.515 0.019 Comparisons 001 - 011 Average 0.030 0.029 0.013 1.044 0.073 1.272 Std Dev 0.002 0.001 0.000 0.834 0.103 1.385 Comparisons 001 - 012 Average 0.029 0.026 0.014 0.746 0.489 0.446 Std Dev 0.003 0.001 0.000 0.779 0.061 1.027 Comparisons 001 - 013 Average 0.029 0.026 0.013 0.624 0.043 0.443 Std Dev 0.002 0.001 0.001 0.976 0.543 1.056 Comparisons 001 - 014 Average 0.028 0.025 0.013 0.180 0.226 0.530 Std Dev 0.003 0.002 0.002 0.688 0.800 1.019 Comparisons 001 - 015 Average 0.029 0.026 0.013 0.682 0.311 0.511 Std Dev 0.004 0.002 0.002 0.311 1.076 1.067 15 Appendix A Comparisons 001 - 016 Average 0.027 0.024 0.013 0.154 0.061 1.217 Std Dev 0.004 0.003 0.001 0.149 0.560 0.019 Comparisons 001 - 017 Average 0.027 0.023 0.013 0.226 0.059 1.255 Std Dev 0.004 0.003 0.001 0.169 0.558 0.014 Comparisons 001 - 018 Average 0.029 0.026 0.013 0.638 0.227 0.463 Std Dev 0.003 0.001 0.001 0.977 0.326 1.058 Comparisons 001 - 019 Average 0.029 0.026 0.013 0.643 0.066 0.471 Std Dev 0.002 0.001 0.001 0.938 0.569 1.080 Comparisons 001 - 020 Average 0.029 0.026 0.013 0.637 0.227 0.463 Std Dev 0.003 0.001 0.001 0.976 0.326 1.055 Comparisons 001 - 021 Average 0.029 0.026 0.013 0.641 0.235 0.471 Std Dev 0.003 0.001 0.001 0.941 0.331 1.081 Comparisons 001 - 022 Average 0.030 0.028 0.014 1.235 0.526 0.356 Std Dev 0.003 0.003 0.000 0.895 0.077 0.053 Comparisons 001 - 023 Average 0.030 0.028 0.014 1.190 0.529 0.277 Std Dev 0.002 0.003 0.000 1.023 0.000 0.000 Comparisons 001 - 024 Average 0.027 0.025 0.012 0.006 0.393 0.525 Std Dev 0.003 0.001 0.000 0.715 0.082 1.045 Comparisons 001 - 025 Average 0.029 0.026 0.014 0.389 0.629 0.524 Std Dev 0.004 0.001 0.001 0.557 0.231 1.027 16 Appendix A Cy2-en/Cd Complex Data Table A.8: Abridged WitsGAFFtyp.txt file ATOM MASS REFERENCE c3 12.01 sp3 C h3 1.008 H bonded to aliphatic carbon with 3 electrwd. group hn 1.008 H bonded to nitrogen atoms ho 1.008 Hydroxyl group cl 35.45 Chlorine n3 14.01 sp3 N with three connected atoms oh 16 Oxygen in hydroxyl group c0 40.08 calcium added J.R 01.04.05 cu2 63.55 copper(II) added HMM 10.02.06 ni2 58.6 Nickel 2+ HMM 14/08/2007 cd2 112.41 Cadmium 2+ SAR 18/04/2008 Table A.9: Abridged WitsGAFFstr.txt file B1 B2 KR REQ REFERENCE c3 c3 303.1 1.535 c3 n3 320.6 1.47 c3 oh 314.1 1.426 cu2 n3a 300.0 1.975 cu2 n3b 300.0 1.975 cu2 oha 150.0 1.970 cu2 ohb 150.0 1.970 ni2 n3a 300.0 2.135 HMM 14/08/2007 ni2 n3b 300.0 2.135 HMM 14/08/2007 ni2 n3c 300.0 2.135 HMM 14/08/2007 ni2 oha 150.0 2.048 HMM 2007 ni2 ohb 150.0 2.048 HMM 2007 ni2 ohc 150.0 2.048 HMM 2007 cd2 n3 300.0 2.390 SAR 18/04/2008 cd2 oh 150.0 2.440 SAR 18/04/2008 cd2 cl 150.0 2.610 SAR 18/04/2008 Table A.10: Abridged WitsGAFFben.txt file A1 A2 A3 KTHETA THETAEQ REFERENCE h1 c3 n3a 49.4 109.92 HAR 24/02/2006 from H1-C3-N3 c3 n3a hn 47.1 109.92 HAR 24/02/2006 from HN-N3-C3 c3 oha ho 47.1 108.16 HAR 24/02/2006 from ho-oh-C3 h1 c3 oha 51.0 109.88 HAR 24/02/2006 from h1-c3-oh c3 c3 oha 67.7 109.43 HAR 24/02/2006 from c3-c3-oh cu2 oh ho 47.1 108.16 HAR 09/03/2006 from c3-oh-ho oh cu2 n3b 72.0 90.000 HAR 09/03/2006 from cobalamins force field n3 cd2 n3 0.00 74.00 SAR 18/04/2008 n3 cd2 oh 0.00 70.00 SAR 18/04/2008 n3 cd2 cl 0.00 90.00 SAR 18/04/2008 oh cd2 cl 0.00 90.00 SAR 18/04/2008 cl cd2 cl 0.00 90.00 SAR 18/04/2008 cd2 n3 c3 64.0 110.90 SAR 18/04/2008 from c3 n3 c3 cd2 oh c3 62.1 113.41 SAR 18/04/2008 from c3 os c3 cd2 n3 hn 47.1 109.92 SAR 18/04/2008 from c3 n3 hn cd2 oh ho 47.1 108.16 SAR 18/04/2008 from c3 oh ho 17 Appendix A Table A.11: Abridged WitsGAFFnbd.txt file ATOM R_STAR EPS REFERENCE hc 1.487 0.0157 OPLS hn 0.600 0.0157 !Ferguson base pair geom. ho 0.000 0.0000 " OPLS Jorgensen, JACS,110,(1988),1657" oh 1.721 0.2104 OPLS c3 1.908 0.1094 OPLS n3 1.824 0.1700 OPLS cl 1.948 0.2650 "Fox, JPCB,102,8070,(98),flex.mdl CHCl3" cu2 1.970 0.0440 Cu(II) preliminary values - PCCP, 2002, 4, 5878. HAR 13/02/2006 ni2 1.960 0.0440 Ni(II) preliminary values - PCCP, 2002, 4, 5878. HMM 14/08/2007 cd2 0.970 0.2600 SAR 18/04/2008 R_Star from corr with ionic radius epsilon from corr with third ionisation E Table A.12: Abridged WitsGAFFtor.txt file T1 T2 T3 T4 HALF_VN GAMMA N REFERENCE ** c3 n3 ** 6 1.80 0.00 3.00 "Junmei et al, 1999 " ** c3 n4 ** 9 1.40 0.00 3.00 "JCC,7,(1986),230 " ** c3 oh ** 3 0.50 0.00 3.00 "JCC,7,(1986),230 " ** oh oh ** 1 1.60 0.00 2.00 hc c3 c3 hc 1 0.15 0.00 3.00 "Junmei et al, 1999 " ni2 n3a c3 c3 1 0.30 0.00 3.00 HMM 2007 based on c3- c3-n3-c3 ni2 n3a c3 h1 1 1.80 0.00 3.00 HMM 2007 based on **- c3-n3-** c3 c3 oha ni2 1 0.50 0.00 3.00 HMM 2007 based on **- c3-oh-** h1 c3 oha ni2 1 0.50 0.00 3.00 HMM 2007 based on **- c3-oh-** ** cd2 ** ** 1 0.00 180.0 1.00 SAR 18/04/2008 Table A.13: Abridged WitsGAFFimp.txt file T1 T2 T3 T4 HALF_VN GAMMA N REFERENCE ** o c o 1.10 180.00 2.00 " JCC,7,(1986),230" ** ** c o 10.50 180.00 2.00 " JCC,7,(1986),230" ** ** n hn 1.10 180.00 2.00 " JCC,7,(1986),230" ** ** n2 Hn 1.10 180.00 2.00 " JCC,7,(1986),230" ** ** na hn 1.10 180.00 2.00 " JCC,7,(1986),230" ** c3 n c3 1.10 180.00 2.00 " JCC,7,(1986),230" ** n2 ca n2 10.50 180.00 2.00 " JCC,7,(1986),230" c3 o c oh 1.10 180.00 2.00 c2 c3 c2 hc 1.10 180.00 2.00 Junmei et al.1999 c2 c3 ca hc 1.10 180.00 2.00 Junmei et al.1999 c2 hc c o 1.10 180.00 2.00 Junmei et al.1999 c3 ca ca n2 1.10 180.00 2.00 c3 ca ca na 1.10 180.00 2.00 hc o c oh 1.10 180.00 2.00 Junmei et al.1999 hc o c os 1.10 180.00 2.00 n2 c2 ca n2 1.10 180.00 2.00 " dac guess, 9/94" n2 ca ca n2 1.10 180.00 2.00 " dac guess, 9/94" na n2 ca n2 1.10 180.00 2.00 " dac, 10/94" ** ** ** ** 1.10 180.00 2.00 " dac, 10/94" ** ** cd2 ** 0.00 180.00 2.00 SAR 18/04/2008 18 Appendix A 19 Table A.14: Energies of the Cy2-en/Cd Complex After the First Simulated Annealing Runs with Various Run Times Compared to the Energy of the XRD Structure Run Time Energy [kcal/mol] XRD structure 22.835 5 ps 18.933 10 ps 19.704 15 ps 19.899 20 ps 18.505 25 ps 18.505 30 ps 25.450 35 ps 19.738 40 ps 25.586 45 ps 19.917 50 ps 19.362 55 ps 20.808 60 ps 19.705 65 ps 18.900 70 ps 18.695 75 ps 19.917 80 ps 18.817 85 ps 19.705 90 ps 19.547 95 ps 18.971 100 ps 18.814 Appendix A Table A.15: Cy2-en/Cd Complex Data After the First Simulated Annealing Run C-C C-N C-O N-Cd O-Cd Cd-Cl C-C-C C-C-N C-C-O C-N-C C-N- Cd C-O- Cd O-Cd- N N-Cd- Cl O-Cd- Cl XRD Cy2en_Cd_000 Average 1.521 1.480 1.439 2.348 2.382 2.494 110.7 111.0 111.4 113.1 112.5 114.5 108.1 116.5 92.5 Std Dev 0.009 0.013 0.006 0.020 0.000 0.4 1.9 1.1 2.4 8.2 51.1 25.1 3.3 Drawn file Cy2en_Cd_001 no charges Average 1.545 1.480 1.432 1.619 3.162 2.799 111.2 110.2 109.3 114.5 112.4 91.7 75.3 115.1 114.6 Std Dev 0.005 0.004 0.000 0.219 0.029 0.4 1.2 0.4 0.0 5.4 15.6 8.8 57.7 MM Cy2en_Cd_002 no charges Average 1.545 1.485 1.431 2.388 2.444 2.610 111.1 111.6 109.1 116.9 108.5 114.7 82.3 104.2 109.2 Std Dev 0.005 0.005 0.000 0.002 0.000 0.6 3.1 1.6 2.6 0.5 13.7 30.8 72.4 ZINDO1 Cy2en_Cd_003 e = 76 Average 1.545 1.480 1.432 1.619 3.162 2.799 111.2 110.2 109.3 114.5 112.4 91.7 75.3 115.1 114.6 Std Dev 0.005 0.004 0.000 0.219 0.029 0.4 1.2 0.4 0.0 5.4 15.6 8.8 57.7 MM w ZINDO1 Cy2en_Cd_004 e = 76 Average 1.545 1.485 1.431 2.388 2.444 2.609 111.1 111.6 109.1 116.9 108.5 114.7 82.3 103.6 108.4 Std Dev 0.005 0.005 0.000 0.001 0.000 0.6 3.0 1.6 2.6 0.5 13.7 30.8 72.2 Annealing Cy2en_Cd_005 r.t. = 5 ps Average 1.544 1.480 1.431 2.391 2.442 2.610 111.2 109.7 109.0 115.1 109.2 113.9 100.3 114.6 103.8 Std Dev 0.005 0.005 0.001 0.003 0.000 0.4 2.6 0.7 0.6 1.0 40.2 39.5 7.6 20 Appendix A Annealing Cy2en_Cd_006 r.t. = 10 ps Average 1.544 1.480 1.431 2.391 2.442 2.610 111.2 109.6 109.0 115.4 109.1 113.9 100.2 146.4 108.5 Std Dev 0.006 0.005 0.002 0.003 0.000 0.4 2.7 1.1 0.4 0.9 40.0 28.1 0.0 Annealing Cy2en_Cd_007 r.t. = 15 ps Average 1.546 1.483 1.432 2.390 2.441 2.609 111.4 110.5 109.3 115.6 108.5 113.4 92.4 107.7 122.5 Std Dev 0.005 0.003 0.000 0.003 0.000 0.5 2.0 0.7 0.1 0.7 28.6 35.6 6.4 Annealing Cy2en_Cd_008 r.t. = 20 ps Average 1.546 1.483 1.431 2.390 2.442 2.609 111.4 110.6 109.1 115.5 108.5 114.0 91.6 88.6 176.8 Std Dev 0.005 0.003 0.002 0.002 0.000 0.5 2.1 0.7 0.0 0.7 27.9 20.8 0.0 Annealing Cy2en_Cd_009 r.t. = 25 ps Average 1.546 1.483 1.431 2.390 2.442 2.609 111.4 110.6 109.1 115.5 108.5 114.0 91.6 88.6 176.8 Std Dev 0.005 0.003 0.002 0.002 0.000 0.5 2.1 0.7 0.0 0.7 27.9 20.8 0.0 Annealing Cy2en_Cd_010 r.t. = 30 ps Average 1.546 1.481 1.430 2.391 2.442 2.610 111.7 109.9 108.8 114.8 108.8 113.8 100.8 93.0 91.8 Std Dev 0.007 0.005 0.002 0.000 0.001 0.8 2.3 1.0 1.1 0.8 40.7 13.0 8.2 Annealing Cy2en_Cd_011 r.t. = 35 ps Average 1.545 1.480 1.432 2.391 2.441 2.609 111.4 110.0 109.3 114.9 108.7 113.3 101.0 97.8 82.0 Std Dev 0.006 0.005 0.000 0.001 0.000 0.4 2.5 0.7 1.1 0.7 40.7 7.3 12.2 Annealing Cy2en_Cd_012 r.t. = 40 ps 21 Appendix A Average 1.546 1.480 1.430 2.391 2.442 2.609 111.7 109.9 108.7 114.9 108.7 113.8 100.6 103.5 85.1 Std Dev 0.007 0.004 0.001 0.000 0.000 0.9 2.7 0.6 1.2 0.7 40.5 11.7 4.0 Annealing Cy2en_Cd_013 r.t. = 45 ps Average 1.545 1.480 1.432 2.390 2.441 2.609 111.5 110.0 109.3 114.8 108.8 113.3 101.1 100.3 73.4 Std Dev 0.006 0.005 0.000 0.001 0.000 0.4 2.4 0.7 1.2 0.6 40.7 2.1 0.0 Annealing Cy2en_Cd_014 r.t. = 50 ps Average 1.546 1.484 1.432 2.390 2.441 2.609 111.5 110.6 109.3 115.5 108.5 113.4 92.5 88.5 175.3 Std Dev 0.005 0.003 0.000 0.002 0.000 0.5 2.0 0.7 0.0 0.7 28.7 20.6 0.0 Annealing Cy2en_Cd_015 r.t. = 55 ps Average 1.546 1.481 1.433 2.390 2.441 2.609 111.6 110.0 109.7 114.9 108.7 113.3 101.1 100.3 73.6 Std Dev 0.006 0.005 0.001 0.000 0.000 0.5 2.4 0.9 1.1 0.6 40.7 2.3 0.0 Annealing Cy2en_Cd_016 r.t. = 60 ps Average 1.545 1.480 1.432 2.391 2.442 2.609 111.5 109.9 109.5 115.1 108.7 113.9 100.6 95.2 90.5 Std Dev 0.006 0.005 0.003 0.000 0.000 0.5 2.7 1.1 1.0 0.8 40.5 9.0 0.0 Annealing Cy2en_Cd_017 r.t. = 65 ps Average 1.546 1.483 1.431 2.390 2.442 2.609 111.4 110.5 109.1 115.5 108.5 114.0 91.8 84.5 119.1 Std Dev 0.004 0.003 0.002 0.002 0.000 0.5 2.1 0.7 0.0 0.7 28.1 18.3 0.0 Annealing Cy2en_Cd_018 r.t. = 70 ps Average 1.546 1.483 1.431 2.390 2.442 2.609 111.4 110.6 109.1 115.5 108.5 114.0 91.7 86.5 147.5 Std Dev 0.005 0.003 0.002 0.002 0.000 0.5 2.1 0.6 0.0 0.7 28.0 19.5 40.2 22 Appendix A Annealing Cy2en_Cd_019 r.t. = 75 ps Average 1.545 1.480 1.432 2.390 2.441 2.609 111.5 110.0 109.3 114.8 108.8 113.3 101.1 100.3 73.4 Std Dev 0.006 0.005 0.000 0.001 0.000 0.4 2.4 0.7 1.2 0.6 40.7 2.2 0.0 Annealing Cy2en_Cd_020 r.t. = 80 ps Average 1.545 1.480 1.431 2.391 2.442 2.609 111.4 109.9 109.1 115.0 108.7 113.9 100.6 94.8 90.8 Std Dev 0.006 0.005 0.002 0.000 0.000 0.4 2.7 0.7 1.0 0.8 40.5 8.9 0.0 Annealing Cy2en_Cd_021 r.t. = 85 ps Average 1.545 1.480 1.432 2.391 2.442 2.609 111.5 109.9 109.5 115.1 108.7 113.9 100.6 95.2 90.5 Std Dev 0.006 0.005 0.003 0.000 0.000 0.5 2.7 1.1 1.0 0.8 40.5 9.0 0.0 Annealing Cy2en_Cd_022 r.t. = 90 ps Average 1.546 1.483 1.432 2.390 2.441 2.609 111.5 110.5 109.3 115.5 108.5 113.4 92.6 86.5 146.3 Std Dev 0.005 0.003 0.000 0.002 0.000 0.5 2.0 0.7 0.0 0.7 28.8 19.5 40.0 Annealing Cy2en_Cd_023 r.t. = 95 ps Average 1.545 1.480 1.431 2.391 2.442 2.609 111.4 110.0 109.1 114.9 108.7 113.8 100.6 98.6 88.6 Std Dev 0.006 0.005 0.002 0.000 0.000 0.4 2.6 0.7 1.1 0.7 40.5 10.0 3.5 Annealing Cy2en_Cd_024 r.t. = 100 ps Average 1.545 1.480 1.431 2.391 2.442 2.609 111.4 109.9 109.1 115.0 108.7 113.9 100.6 94.9 90.8 Std Dev 0.006 0.005 0.002 0.000 0.000 0.4 2.7 0.7 1.0 0.8 40.5 8.9 0.0 Comparisons 000 - 001 Average 0.024 0.004 0.008 0.040 0.062 0.115 0.4 0.5 2.3 3.8 4.0 0.2 25.8 12.3 16.7 Std Dev 0.004 0.008 0.006 0.019 0.000 0.2 1.2 0.5 0.2 7.8 37.4 5.7 69.1 23 Appendix A Comparisons 000 - 003 Average 0.024 0.000 0.007 0.729 0.780 0.304 0.4 0.9 2.1 1.4 0.0 22.9 32.8 1.4 22.1 Std Dev 0.004 0.009 0.006 0.199 0.028 0.0 0.6 0.7 2.4 2.8 35.5 16.3 54.4 Comparisons 000 - 004 Average 0.024 0.004 0.008 0.040 0.062 0.115 0.4 0.5 2.3 3.8 4.0 0.2 25.8 12.9 15.9 Std Dev 0.004 0.008 0.006 0.019 0.000 0.2 1.2 0.5 0.1 7.7 37.4 5.7 69.0 Comparisons 000 - 005 Average 0.023 0.000 0.008 0.043 0.060 0.115 0.5 1.3 2.4 2.0 3.3 0.6 7.8 1.9 11.3 Std Dev 0.004 0.008 0.004 0.018 0.000 0.0 0.7 0.5 1.8 7.2 10.9 14.4 4.3 Comparisons 000 - 006 Average 0.023 0.000 0.008 0.043 0.060 0.115 0.5 1.4 2.4 2.3 3.4 0.6 7.9 29.9 16.0 Std Dev 0.003 0.008 0.004 0.018 0.000 0.0 0.8 0.1 2.0 7.3 11.1 3.0 3.3 Comparisons 000 - 007 Average 0.025 0.003 0.007 0.042 0.059 0.115 0.7 0.5 2.0 2.5 4.0 1.2 15.7 8.8 30.0 Std Dev 0.005 0.010 0.005 0.018 0.000 0.1 0.2 0.4 2.4 7.5 22.5 10.5 3.2 Comparisons 000 - 008 Average 0.024 0.003 0.008 0.042 0.060 0.115 0.7 0.5 2.3 2.4 4.0 0.6 16.5 27.9 84.4 Std Dev 0.005 0.011 0.004 0.018 0.000 0.1 0.2 0.5 2.4 7.5 23.2 4.3 3.3 Comparisons 000 - 009 Average 0.024 0.003 0.008 0.042 0.060 0.115 0.7 0.5 2.3 2.4 4.0 0.6 16.5 27.9 84.3 Std Dev 0.005 0.011 0.004 0.018 0.000 0.1 0.2 0.5 2.4 7.5 23.2 4.3 3.3 Comparisons 000 - 010 Average 0.025 0.001 0.008 0.043 0.060 0.115 1.0 1.1 2.5 1.7 3.6 0.7 7.3 23.4 0.7 Std Dev 0.002 0.008 0.004 0.020 0.001 0.4 0.4 0.2 1.3 7.5 10.4 12.1 4.9 24 Appendix A Comparisons 000 - 011 Average 0.024 0.000 0.007 0.042 0.059 0.115 0.7 1.1 2.1 1.8 3.8 1.2 7.1 18.7 10.5 Std Dev 0.004 0.008 0.006 0.020 0.000 0.0 0.7 0.4 1.3 7.5 10.4 17.8 9.0 Comparisons 000 - 012 Average 0.025 0.000 0.009 0.042 0.059 0.114 1.0 1.1 2.6 1.8 3.8 0.7 7.5 13.0 7.4 Std Dev 0.002 0.009 0.005 0.020 0.000 0.5 0.8 0.5 1.2 7.6 10.6 13.4 0.7 Comparisons 000 - 013 Average 0.024 0.000 0.007 0.042 0.059 0.115 0.7 1.0 2.0 1.7 3.7 1.2 7.1 16.2 19.1 Std Dev 0.004 0.008 0.005 0.020 0.000 0.0 0.5 0.4 1.3 7.7 10.4 23.0 3.3 Comparisons 000 - 014 Average 0.025 0.004 0.007 0.042 0.059 0.115 0.7 0.5 2.0 2.4 4.0 1.2 15.6 28.0 82.9 Std Dev 0.004 0.010 0.005 0.018 0.000 0.1 0.1 0.5 2.4 7.5 22.4 4.5 3.3 Comparisons 000 - 015 Average 0.024 0.000 0.006 0.042 0.059 0.114 0.8 1.1 1.6 1.8 3.7 1.2 7.0 16.2 18.9 Std Dev 0.003 0.009 0.005 0.020 0.000 0.1 0.5 0.2 1.3 7.7 10.4 22.8 3.3 Comparisons 000 - 016 Average 0.024 0.000 0.007 0.043 0.060 0.115 0.8 1.2 1.9 2.0 3.8 0.7 7.5 21.3 1.9 Std Dev 0.003 0.009 0.002 0.020 0.000 0.1 0.8 0.1 1.5 7.4 10.5 16.1 3.3 Comparisons 000 - 017 Average 0.024 0.003 0.008 0.042 0.060 0.115 0.7 0.5 2.3 2.4 4.0 0.5 16.3 32.0 26.7 Std Dev 0.005 0.010 0.004 0.018 0.000 0.1 0.2 0.5 2.4 7.6 23.0 6.8 3.3 Comparisons 000 - 018 Average 0.024 0.003 0.008 0.042 0.060 0.115 0.7 0.5 2.3 2.4 4.0 0.6 16.4 30.0 55.1 Std Dev 0.005 0.010 0.004 0.018 0.000 0.1 0.2 0.5 2.4 7.5 23.1 5.6 36.9 25 Appendix A 26 Comparisons 000 - 019 Average 0.024 0.000 0.007 0.042 0.059 0.115 0.7 1.0 2.0 1.7 3.7 1.2 7.0 16.2 19.1 Std Dev 0.004 0.008 0.005 0.020 0.000 0.0 0.5 0.4 1.3 7.7 10.4 22.9 3.2 Comparisons 000 - 020 Average 0.024 0.000 0.008 0.043 0.060 0.115 0.6 1.1 2.3 1.9 3.8 0.7 7.5 21.6 1.6 Std Dev 0.004 0.008 0.004 0.020 0.000 0.0 0.8 0.4 1.4 7.4 10.6 16.2 3.3 Comparisons 000 - 021 Average 0.024 0.000 0.007 0.043 0.060 0.115 0.8 1.2 1.9 2.0 3.8 0.7 7.5 21.3 2.0 Std Dev 0.003 0.009 0.002 0.020 0.000 0.1 0.8 0.1 1.5 7.4 10.5 16.1 3.3 Comparisons 000 - 022 Average 0.025 0.003 0.007 0.042 0.059 0.115 0.7 0.5 2.0 2.4 4.0 1.2 15.5 30.0 53.8 Std Dev 0.005 0.010 0.005 0.018 0.000 0.1 0.1 0.5 2.4 7.6 22.3 5.6 36.7 Comparisons 000 - 023 Average 0.024 0.000 0.008 0.043 0.060 0.115 0.7 1.1 2.3 1.8 3.7 0.7 7.5 17.9 3.9 Std Dev 0.004 0.009 0.004 0.020 0.000 0.0 0.7 0.4 1.3 7.5 10.6 15.1 0.2 Comparisons 000 - 024 Average 0.024 0.000 0.008 0.043 0.060 0.115 0.7 1.1 2.3 1.9 3.8 0.7 7.5 21.6 1.6 Std Dev 0.004 0.008 0.004 0.020 0.000 0.1 0.8 0.4 1.4 7.4 10.6 16.2 3.3 Appendix A Table A.16: Energies of the Cy2-en/Cd Complex After the Second Simulated Annealing Runs with Various Run Times Compared to the Energy of the XRD Structure Run Time Energy [kcal/mol] XRD structure 22.835 Sample 1: 5 ps 20.034 Sample 1: 10 ps 19.372 Sample 1: 100 ps 18.597 Sample 2: 5 ps 25.083 Sample 2: 10 ps 23.919 Sample 2: 100 ps 18.951 Sample 3: 5 ps 21.589 Sample 3: 10 ps 18.951 Sample 3: 100 ps 25.822 Sample 4: 5 ps 19.559 Sample 4: 10 ps 26.551 Sample 4: 100 ps 21.329 Sample 5: 5 ps 20.034 Sample 5: 10 ps 19.753 Sample 5: 100 ps 18.497 27 Appendix A Table A.17: Cy2-en/Cd Complex Data After the Second Simulated Annealing Process C-C C-N C-O N-Cd O-Cd Cd-Cl C-C-C C-C-N C-C-O C-N-C C-N- Cd C-O- Cd O-Cd- N N-Cd- Cl O-Cd- Cl XRD Cy2en_Cd_000 Average 1.521 1.480 1.439 2.348 2.382 2.494 110.7 111.0 111.4 113.1 112.5 114.5 108.1 116.5 92.5 Std Dev 0.009 0.013 0.006 0.020 0.000 0.4 1.9 1.1 2.4 8.2 51.1 25.1 3.3 Annealing Cy2en_Cd_035 Sample 1 r.t. = 5 ps Average 1.545 1.481 1.432 2.392 2.442 2.610 111.5 110.0 109.3 115.2 109.4 113.2 100.8 150.1 70.9 Std Dev 0.006 0.006 0.000 0.002 0.000 0.5 3.0 0.8 0.7 1.7 40.5 9.7 0.0 Annealing Cy2en_Cd_025 Sample 1 r.t. = 10 ps Average 1.546 1.484 1.432 2.390 2.441 2.609 111.5 110.6 109.3 115.5 108.5 113.4 92.5 88.5 175.4 Std Dev 0.005 0.003 0.000 0.002 0.000 0.5 2.0 0.7 0.0 0.7 28.7 20.6 0.0 Annealing Cy2en_Cd_026 Sample 1 r.t. = 100 ps Average 1.544 1.481 1.431 2.391 2.442 2.610 111.2 109.9 109.0 114.9 109.3 114.0 100.4 82.1 100.1 Std Dev 0.005 0.005 0.001 0.003 0.000 0.4 2.4 0.7 0.7 1.1 40.3 5.9 0.0 Annealing Cy2en_Cd_036 Sample 2 r.t. = 5 ps Average 1.547 1.481 1.431 2.391 2.442 2.611 112.0 110.4 109.0 114.4 109.0 113.9 100.8 78.9 101.1 Std Dev 0.006 0.006 0.002 0.001 0.000 1.2 2.1 0.7 1.3 0.9 40.8 6.1 0.0 Annealing Cy2en_Cd_027 Sample 2 r.t. = 10 ps Average 1.546 1.483 1.431 2.390 2.443 2.610 111.6 110.5 108.8 115.5 108.4 114.2 89.8 113.8 111.2 Std Dev 0.005 0.002 0.002 0.004 0.000 0.8 2.1 0.4 0.4 1.1 25.3 39.3 76.1 28 Appendix A Annealing Cy2en_Cd_028 Sample 2 r.t. = 100 ps Average 1.545 1.480 1.431 2.391 2.442 2.609 111.4 110.0 109.1 114.9 108.7 113.8 100.6 98.6 88.8 Std Dev 0.006 0.005 0.002 0.000 0.000 0.4 2.6 0.7 1.1 0.7 40.5 10.1 3.3 Annealing Cy2en_Cd_037 Sample 3 r.t. = 5 ps Average 1.546 1.483 1.432 2.388 2.445 2.610 111.3 111.6 109.3 116.2 108.8 114.9 82.1 126.1 57.7 Std Dev 0.004 0.006 0.000 0.001 0.000 0.5 2.2 0.3 3.4 0.7 13.7 22.3 0.0 Annealing Cy2en_Cd_029 Sample 3 r.t. = 10 ps Average 1.545 1.480 1.431 2.391 2.442 2.609 111.4 110.0 109.1 114.9 108.7 113.8 100.6 98.6 88.8 Std Dev 0.006 0.005 0.002 0.000 0.000 0.4 2.6 0.7 1.1 0.7 40.5 10.1 3.3 Annealing Cy2en_Cd_030 Sample 3 r.t. = 100 ps Average 1.546 1.479 1.430 2.392 2.444 2.610 111.8 109.7 109.2 115.4 109.1 111.7 101.2 145.4 107.7 Std Dev 0.006 0.004 0.003 0.003 0.000 1.0 3.1 2.0 0.6 0.9 40.6 26.9 0.0 Annealing Cy2en_Cd_038 Sample 4 r.t. = 5 ps Average 1.546 1.483 1.432 2.390 2.441 2.609 111.5 110.5 109.3 115.5 108.5 113.4 92.6 86.5 146.3 Std Dev 0.005 0.003 0.000 0.002 0.000 0.5 2.0 0.7 0.0 0.7 28.9 19.5 39.9 Annealing Cy2en_Cd_031 Sample 4 r.t. = 10 ps Average 1.546 1.480 1.432 2.390 2.441 2.609 111.7 109.9 109.4 114.8 108.8 113.3 101.1 100.1 74.1 Std Dev 0.007 0.005 0.000 0.001 0.000 0.7 2.2 0.8 1.2 0.6 40.7 2.7 0.1 Annealing Cy2en_Cd_032 Sample 4 r.t. = 100 ps Average 1.545 1.483 1.432 2.389 2.441 2.609 111.3 110.9 109.4 115.8 109.3 113.3 97.0 80.1 140.5 29 Appendix A Std Dev 0.004 0.004 0.000 0.003 0.000 0.5 2.2 0.9 0.1 1.3 34.8 13.0 25.4 Annealing Cy2en_Cd_039 Sample 5 r.t. = 5 ps Average 1.545 1.481 1.432 2.392 2.442 2.610 111.5 110.0 109.3 115.2 109.4 113.2 100.8 150.1 70.9 Std Dev 0.006 0.006 0.000 0.002 0.000 0.5 3.0 0.8 0.7 1.7 40.5 9.7 0.0 Annealing Cy2en_Cd_033 Sample 5 r.t. = 10 ps Average 1.544 1.480 1.432 2.391 2.442 2.610 111.2 109.6 109.2 115.3 109.1 113.4 100.6 122.9 88.4 Std Dev 0.006 0.005 0.001 0.003 0.000 0.4 2.6 0.7 0.6 1.0 40.2 30.7 28.7 Annealing Cy2en_Cd_034 Sample 5 r.t. = 100 ps Average 1.546 1.483 1.431 2.390 2.442 2.609 111.4 110.6 109.1 115.5 108.5 114.0 91.6 88.6 176.8 Std Dev 0.005 0.003 0.002 0.002 0.000 0.5 2.0 0.6 0.0 0.7 27.8 20.8 0.0 Comparisons 000 - 035 Average 0.024 0.001 0.007 0.043 0.060 0.116 0.8 1.1 2.1 2.1 3.0 1.3 7.3 33.6 21.6 Std Dev 0.003 0.007 0.005 0.018 0.000 0.2 1.1 0.3 1.8 6.5 10.6 15.4 3.2 Comparisons 000 - 025 Average 0.025 0.004 0.007 0.042 0.059 0.115 0.7 0.5 2.0 2.4 4.0 1.2 15.6 28.0 82.9 Std Dev 0.005 0.010 0.005 0.018 0.000 0.1 0.1 0.4 2.4 7.5 22.4 4.5 3.3 Comparisons 000 - 026 Average 0.023 0.001 0.008 0.043 0.060 0.115 0.4 1.2 2.4 1.8 3.2 0.6 7.7 34.4 7.6 Std Dev 0.004 0.008 0.004 0.018 0.000 0.0 0.6 0.5 1.7 7.1 10.8 19.2 3.3 Comparisons 000 - 036 Average 0.025 0.001 0.008 0.043 0.060 0.116 1.2 0.7 2.3 1.3 3.5 0.6 7.3 37.6 8.7 Std Dev 0.003 0.008 0.003 0.020 0.000 0.8 0.3 0.5 1.1 7.3 10.2 19.0 3.3 30 Appendix A Comparisons 000 - 027 Average 0.025 0.003 0.008 0.041 0.061 0.115 0.9 0.6 2.5 2.4 4.0 0.4 18.3 2.7 18.8 Std Dev 0.004 0.011 0.004 0.016 0.000 0.4 0.2 0.7 2.1 7.1 25.8 14.2 72.8 Comparisons 000 - 028 Average 0.024 0.000 0.008 0.043 0.059 0.115 0.7 1.1 2.3 1.8 3.7 0.7 7.5 17.9 3.7 Std Dev 0.004 0.009 0.004 0.020 0.000 0.0 0.7 0.4 1.3 7.5 10.6 15.0 0.0 Comparisons 000 - 037 Average 0.024 0.003 0.007 0.040 0.063 0.115 0.6 0.6 2.1 3.1 3.7 0.4 26.0 9.6 34.8 Std Dev 0.005 0.007 0.005 0.020 0.000 0.2 0.4 0.8 1.0 7.5 37.4 2.8 3.3 Comparisons 000 - 029 Average 0.024 0.000 0.008 0.043 0.059 0.115 0.7 1.1 2.3 1.8 3.7 0.7 7.5 17.9 3.7 Std Dev 0.004 0.009 0.004 0.020 0.000 0.0 0.7 0.4 1.3 7.5 10.6 15.0 0.0 Comparisons 000 - 030 Average 0.024 0.001 0.009 0.044 0.061 0.115 1.1 1.3 2.2 2.2 3.4 2.9 6.9 28.9 15.3 Std Dev 0.003 0.009 0.003 0.017 0.000 0.6 1.3 0.9 1.8 7.4 10.5 1.8 3.3 Comparisons 000 - 038 Average 0.025 0.003 0.007 0.042 0.059 0.115 0.7 0.5 2.0 2.4 4.0 1.2 15.5 30.0 53.8 Std Dev 0.005 0.010 0.005 0.018 0.000 0.1 0.1 0.4 2.4 7.6 22.2 5.6 36.6 Comparisons 000 - 031 Average 0.025 0.000 0.007 0.042 0.059 0.115 1.0 1.2 1.9 1.7 3.7 1.2 7.0 16.4 18.4 Std Dev 0.002 0.009 0.005 0.020 0.000 0.3 0.3 0.3 1.2 7.7 10.4 22.4 3.2 Comparisons 000 - 032 Average 0.024 0.003 0.006 0.041 0.058 0.115 0.6 0.1 2.0 2.7 3.1 1.2 11.1 36.4 48.0 Std Dev 0.005 0.010 0.005 0.018 0.000 0.1 0.3 0.3 2.3 6.9 16.3 12.1 22.1 Comparisons 000 - 039 31 Appendix A 32 Average 0.024 0.001 0.007 0.043 0.060 0.116 0.8 1.1 2.1 2.1 3.0 1.3 7.3 33.6 21.6 Std Dev 0.003 0.007 0.005 0.018 0.000 0.2 1.1 0.3 1.8 6.5 10.6 15.4 3.2 Comparisons 000 - 033 Average 0.022 0.000 0.007 0.043 0.060 0.115 0.5 1.4 2.1 2.2 3.3 1.1 7.5 6.5 4.1 Std Dev 0.004 0.008 0.005 0.018 0.000 0.0 0.8 0.4 1.8 7.2 10.9 5.6 25.5 Comparisons 000 - 034 Average 0.024 0.003 0.008 0.042 0.060 0.115 0.7 0.5 2.3 2.4 4.0 0.6 16.5 27.9 84.4 Std Dev 0.005 0.011 0.004 0.018 0.000 0.1 0.2 0.5 2.4 7.5 23.2 4.3 3.3 Appendix A Table A.18: Abridged WitsGAFFtyp.txt file for the first geometry optimisation run ATOM MASS REFERENCE cd2 112.41 Cadmium 2+ SAR 18/04/2008 clx 35.45 Chlorine coordinated to cd2 in an axial manner SAR 06/05/2008 cly 35.45 Chlorine coordinated to cd2 in an axial manner SAR 06/05/2008 n3x 14.01 nitrogen coordinated to cd2 and trans to cly SAR 06/05/2008 n3y 14.01 nitrogen coordinated to cd2 and at right angle to cly SAR 06/05/2008 Table A.19: Abridged WitsGAFFstr.txt file for the first geometry optimisation run B1 B2 KR REQ REFERENCE cd2 n3 320.0 2.390 SAR 01/05/2008 cd2 oh 175.0 2.440 SAR 01/05/2008 cd2 cl 200.0 2.610 SAR 01/05/2008 cd2 n3x 350.0 2.390 SAR 06/05/2008 cd2 n3y 350.0 2.390 SAR 06/05/2008 cd2 oh 150.0 2.440 SAR 06/05/2008 cd2 clx 200.0 2.610 SAR 06/05/2008 cd2 cly 200.0 2.610 SAR 06/05/2008 hn n3x 394.1 1.018 SAR 06/05/2008 hn n3y 394.1 1.018 SAR 06/05/2008 Table A.20: Abridged WitsGAFFben.txt file for the first geometry optimisation run A1 A2 A3 KTHETA THETAEQ REFERENCE n3x cd2 n3y 20.00 90.00 SAR 06/05/2008 co-planar nitrogens n3x cd2 oh 70.00 90.00 SAR 06/05/2008 co-planar cis atoms n3y cd2 oh 70.00 180.00 SAR 06/05/2008 co-planar trans atoms n3x cd2 cly 50.00 180.00 SAR 06/05/2008 co-planar trans atoms n3y cd2 cly 50.00 90.00 SAR 06/05/2008 co-planar cis atoms oh cd2 cly 50.00 90.00 SAR 06/05/2008 co-planar trans atoms clx cd2 cly 50.00 90.00 SAR 06/05/2008 axial and equatorial atoms oh cd2 clx 50.00 90.00 SAR 06/05/2008 axial cl to equatorial o n3x cd2 clx 50.00 90.00 SAR 06/05/2008 axial cl to equatorial n3x n3y cd2 clx 50.00 90.00 SAR 06/05/2008 axial cl to equatorial n3y cd2 n3x c3 64.0 110.90 SAR 06/05/2008 from c3 n3 c3 cd2 n3y c3 64.0 110.90 SAR 06/05/2008 from c3 n3 c3 cd2 oh c3 62.1 113.41 SAR 06/05/2008 from c3 os c3 cd2 n3x hn 47.1 109.92 SAR 06/05/2008 from c3 n3 hn cd2 n3y hn 47.1 109.92 SAR 06/05/2008 from c3 n3 hn c3 n3x hn 47.1 109.92 SAR 06/05/2008 from c3 n3 hn c3 n3y hn 47.1 109.92 SAR 06/05/2008 from c3 n3 hn 33 Appendix A Table A.21: Abridged WitsGAFFnbd.txt file for the first geometry optimisation run ATOM R_STAR EPS REFERENCE cd2 0.970 0.2600 SAR 18/04/2008 R_Star from corr with ionic radius epsilon from corr with third ionisation E n3x 1.824 0.1700 SAR 06/05/2008 n3y 1.824 0.1700 SAR 06/05/2008 clx 1.948 0.2650 SAR 06/05/2008 cly 1.948 0.2650 SAR 06/05/2008 Table A.22: Abridged WitsGAFFtor.txt file for the first geometry optimisation run T1 T2 T3 T4 HALF_VN GAMMA N REFERENCE ** cd2 ** ** 1 0.00 180.0 1.00 SAR 18/04/2008 clx cd2 oh ho 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero clx cd2 oh c3 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero clx cd2 n3x hn 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero clx cd2 n3x c3 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero clx cd2 n3y hn 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero clx cd2 n3y c3 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero cly cd2 oh ho 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero cly cd2 oh c3 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero cly cd2 n3x hn 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero cly cd2 n3x c3 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero cly cd2 n3y hn 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero cly cd2 n3y c3 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero n3x c3 c3 n3y 1 1.40 0.00 3.00 SAR 06/05/2008 based on **-c3-c3-** n3x cd2 oh ho 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero n3y cd2 oh ho 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero n3x cd2 oh c3 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero n3y cd2 oh c3 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero n3x cd2 n3y hn 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero n3y cd2 n3x hn 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero n3x cd2 n3y c3 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero n3y cd2 n3x c3 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero n3x c3 c3 hc 1 1.40 0.00 3.00 SAR 06/05/2008 based on **-c3-c3-** n3y c3 c3 hc 1 1.40 0.00 3.00 SAR 06/05/2008 based on **-c3-c3-** 34 Appendix A n3x c3 c3 h1 1 1.40 0.00 3.00 SAR 06/05/2008 based on **-c3-c3-** n3y c3 c3 h1 1 1.40 0.00 3.00 SAR 06/05/2008 based on **-c3-c3-** hn n3x cd2 oh 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero hn n3y cd2 oh 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero c3 c3 n3x hn 6 1.80 0.00 3.00 SAR 06/05/2008 based on **-c3-n3-** c3 c3 n3y hn 6 1.80 0.00 3.00 SAR 06/05/2008 based on **-c3-n3-** h1 c3 n3x hn 6 1.80 0.00 3.00 SAR 06/05/2008 based on **-c3-n3-** h1 c3 n3y hn 6 1.80 0.00 3.00 SAR 06/05/2008 based on **-c3-n3-** c3 n3x cd2 oh 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero c3 n3y cd2 oh 1 0.00 180.0 2.00 SAR 06/05/2008 all torsions **-**-cd2-** set to zero c3 c3 n3x c3 6 1.80 0.00 3.00 SAR 06/05/2008 based on **-c3-n3-** c3 c3 n3y c3 6 1.80 0.00 3.00 SAR 06/05/2008 based on **-c3-n3-** h1 c3 n3x c3 6 1.80 0.00 3.00 SAR 06/05/2008 based on **-c3-n3-** h1 c3 n3y c3 6 1.80 0.00 3.00 SAR 06/05/2008 based on **-c3-n3-** cd2 n3x c3 c3 1 0.30 0.00 3.00 SAR 06/05/2008 based on c3-c3-n3-c3 cd2 n3y c3 c3 1 0.30 0.00 3.00 SAR 06/05/2008 based on c3-c3-n3-c3 cd2 n3x c3 h1 1 1.80 0.00 3.00 SAR 06/05/2008 based on **-c3-n3-** cd2 n3y c3 h1 1 1.80 0.00 3.00 SAR 06/05/2008 based on **-c3-n3-** Table A.23: Abridged WitsGAFFben.txt file for the second geometry optimisation run A1 A2 A3 KTHETA THETAEQ REFERENCE n3x cd2 cly 50.00 96.00 SAR 06/05/2008 co-planar trans atoms n3y cd2 cly 50.00 106.00 SAR 06/05/2008 co-planar cis atoms oh cd2 cly 50.00 95.00 SAR 06/05/2008 co-planar trans atoms clx cd2 cly 50.00 106.00 SAR 06/05/2008 axial and equatorial atoms oh cd2 clx 50.00 90.00 SAR 06/05/2008 axial cl to equatorial o n3x cd2 clx 50.00 153.00 SAR 06/05/2008 axial cl to equatorial n3x n3y cd2 clx 50.00 111.00 SAR 06/05/2008 axial cl to equatorial n3y cd2 n3x c3 64.0 110.00 SAR 06/05/2008 from c3 n3 c3 cd2 n3y c3 64.0 115.00 SAR 06/05/2008 from c3 n3 c3 cd2 oh c3 62.1 115.00 SAR 06/05/2008 from c3 os c3 cd2 n3x hn 47.1 107.00 SAR 06/05/2008 from c3 n3 hn cd2 n3y hn 47.1 105.00 SAR 06/05/2008 from c3 n3 hn c3 n3x hn 47.1 107.00 SAR 06/05/2008 from c3 n3 hn c3 n3y hn 47.1 105.00 SAR 06/05/2008 from c3 n3 hn 35 Appendix A Table A.24: Abridged WitsGAFFstr.txt file for the third geometry optimisation run B1 B2 KR REQ REFERENCE cd2 n3x 350.0 2.390 SAR 06/05/2008 cd2 n3y 350.0 2.390 SAR 06/05/2008 cd2 oh 150.0 2.440 SAR 06/05/2008 cd2 clx 225.0 2.605 SAR 07/05/2008 cd2 cly 225.0 2.605 SAR 07/05/2008 hn n3x 394.1 1.018 SAR 06/05/2008 hn n3y 394.1 1.018 SAR 06/05/2008 Table A.25: Abridged WitsGAFFben.txt file for the third geometry optimisation run A1 A2 A3 KTHETA THETAEQ REFERENCE cd2 n3x c3 64.0 110.00 SAR 06/05/2008 from c3 n3 c3 cd2 n3y c3 64.0 115.00 SAR 06/05/2008 from c3 n3 c3 cd2 oh c3 62.1 115.00 SAR 06/05/2008 from c3 os c3 cd2 n3x hn 47.1 107.00 SAR 06/05/2008 from c3 n3 hn cd2 n3y hn 47.1 105.00 SAR 06/05/2008 from c3 n3 hn c3 n3x hn 47.1 109.92 SAR 07/05/2008 from c3 n3 hn c3 n3y hn 47.1 109.92 SAR 07/05/2008 from c3 n3 hn Table A.26: Abridged WitsGAFFstr.txt file for the fourth geometry optimisation run B1 B2 KR REQ REFERENCE cd2 n3x 350.0 2.390 SAR 06/05/2008 cd2 n3y 350.0 2.390 SAR 06/05/2008 cd2 oh 150.0 2.440 SAR 06/05/2008 cd2 clx 250.0 2.590 SAR 07/05/2008 cd2 cly 250.0 2.590 SAR 07/05/2008 hn n3x 394.1 1.018 SAR 06/05/2008 hn n3y 394.1 1.018 SAR 06/05/2008 Table A.27: Abridged WitsGAFFben.txt file for the fourth geometry optimisation run A1 A2 A3 KTHETA THETAEQ REFERENCE oh cd2 cly 50.00 90.00 SAR 07/05/2008 co-planar trans atoms oh cd2 clx 50.00 90.00 SAR 06/05/2008 axial cl to equatorial o n3x cd2 clx 50.00 153.00 SAR 06/05/2008 axial cl to equatorial n3x n3y cd2 clx 50.00 111.00 SAR 06/05/2008 axial cl to equatorial n3y cd2 n3x c3 64.0 110.00 SAR 06/05/2008 from c3 n3 c3 cd2 n3y c3 64.0 115.00 SAR 06/05/2008 from c3 n3 c3 cd2 oh c3 62.1 115.00 SAR 06/05/2008 from c3 os c3 cd2 n3x hn 47.1 107.00 SAR 06/05/2008 from c3 n3 hn cd2 n3y hn 47.1 105.00 SAR 06/05/2008 from c3 n3 hn c3 n3x hn 47.1 109.92 SAR 07/05/2008 from c3 n3 hn c3 n3y hn 47.1 109.92 SAR 07/05/2008 from c3 n3 hn 36 Appendix A 37 Table A.28: Abridged WitsGAFFstr.txt file for the fifth geometry optimisation run B1 B2 KR REQ REFERENCE cd2 oh 150.0 2.440 SAR 01/05/2008 cd2 n3x 300.0 2.390 SAR 07/05/2008 cd2 n3y 300.0 2.390 SAR 07/05/2008 cd2 clx 250.0 2.500 SAR 07/05/2008 cd2 cly 250.0 2.500 SAR 07/05/2008 Table A.29: Abridged WitsGAFFstr.txt file for the sixth geometry optimisation run B1 B2 KR REQ REFERENCE cd2 oh 125.0 2.440 SAR 01/05/2008 cd2 n3x 275.0 2.390 SAR 07/05/2008 cd2 n3y 275.0 2.390 SAR 07/05/2008 cd2 clx 250.0 2.500 SAR 07/05/2008 cd2 cly 250.0 2.500 SAR 07/05/2008 Table A.30: Abridged WitsGAFFstr.txt file for the seventh geometry optimisation run B1 B2 KR REQ REFERENCE cd2 oh 125.0 2.400 SAR 01/05/2008 cd2 n3x 275.0 2.380 SAR 07/05/2008 cd2 n3y 275.0 2.380 SAR 07/05/2008 cd2 clx 250.0 2.500 SAR 07/05/2008 cd2 cly 250.0 2.500 SAR 07/05/2008 hn n3x 394.1 1.018 SAR 06/05/2008 hn n3y 394.1 1.018 SAR 06/05/2008 Appendix A Table A.31: Cy2-en/Cd Data After the Various Geometry Optimisations C-C C-N C-O N-Cd O-Cd Cd- Cl C-C-C C-C-N C-C-O C-N-C C-N-Cd C-O-Cd O-Cd-N N-Cd-Cl O-Cd- Cl XRD Cy2en_Cd_040 Average 1.521 1.480 1.439 2.348 2.382 2.494 110.7 111.0 111.4 113.1 112.5 114.5 108.1 116.5 92.5 Std Dev 0.009 0.013 0.006 0.020 0.000 0.4 1.9 1.1 2.4 8.2 51.1 25.1 3.3 Geom op Cy2en_Cd_041 initial guess Average 1.550 1.492 1.448 2.356 2.390 2.611 111.2 110.6 110.8 115.9 106.0 104.4 120.7 114.9 92.9 run 1 Std Dev 0.014 0.007 0.022 0.030 0.000 0.2 1.6 2.6 5.7 6.0 56.0 42.7 6.3 Geom op Cy2en_Cd_042 run 2 Average 1.550 1.490 1.446 2.360 2.395 2.610 111.195 110.444 110.571 116.932 109.226 105.061 118.100 115.823 48.040 Std Dev 0.013 0.003 0.018 0.023 0.001 0.313 1.773 2.305 3.196 8.123 53.517 25.616 55.378 Geom op Cy2en_Cd_043 run 3 Average 1.550 1.491 1.446 2.360 2.394 2.605 111.199 110.476 110.565 116.153 108.436 105.089 118.462 116.148 85.857 Std Dev 0.013 0.002 0.018 0.023 0.001 0.345 2.083 2.336 3.379 7.828 53.976 25.449 2.426 Geom op Cy2en_Cd_044 run 4 Average 1.545 1.485 1.432 2.386 2.431 2.590 111.109 109.415 109.618 112.411 111.499 112.639 106.824 117.439 90.592 Std Dev 0.004 0.003 0.001 0.002 0.001 0.445 2.584 0.777 0.239 3.815 49.391 24.721 1.191 Geom op Cy2en_Cd_045 run 5 Average 1.545 1.485 1.432 2.386 2.430 2.500 111.108 109.446 109.616 112.371 111.548 112.658 106.829 117.452 90.527 Std Dev 0.004 0.003 0.001 0.003 0.001 0.445 2.615 0.784 0.277 3.916 49.389 24.701 1.165 Geom op Cy2en_Cd_046 run 6 Average 1.545 1.485 1.432 2.385 2.428 2.500 111.108 109.441 109.616 112.369 111.549 112.681 106.842 117.452 90.523 Std Dev 0.004 0.003 0.001 0.003 0.001 0.443 2.622 0.787 0.280 3.916 49.386 24.704 1.154 38 Appendix A 39 Geom op Cy2en_Cd_047 run 7 Average 1.545 1.484 1.432 2.376 2.391 2.500 111.100 109.350 109.609 112.309 111.585 113.075 107.156 117.444 90.409 Std Dev 0.003 0.003 0.001 0.002 0.001 0.425 2.764 0.872 0.296 3.911 49.347 24.765 0.932 Comparisons 040 - 041 Average 0.029 0.012 0.009 0.007 0.008 0.117 0.476 0.469 0.604 2.768 6.428 10.172 12.563 1.543 0.423 Std Dev 0.005 0.006 0.016 0.010 0.000 0.184 0.253 1.502 3.289 2.209 4.893 17.634 3.074 Comparisons 040 - 042 Average 0.028 0.010 0.007 0.012 0.013 0.116 0.457 0.605 0.799 3.824 3.240 9.479 9.997 0.657 44.438 Std Dev 0.003 0.011 0.013 0.003 0.001 0.079 0.102 1.164 0.769 0.109 2.422 0.515 52.102 Comparisons 040 - 043 Average 0.028 0.011 0.007 0.012 0.012 0.111 0.462 0.573 0.805 3.045 4.030 9.450 10.359 0.332 6.621 Std Dev 0.004 0.011 0.013 0.003 0.001 0.046 0.207 1.195 0.952 0.405 2.880 0.349 0.850 Comparisons 040 - 044 Average 0.024 0.004 0.007 0.038 0.049 0.096 0.372 1.635 1.752 0.696 0.967 1.901 1.279 0.958 1.886 Std Dev 0.006 0.010 0.004 0.018 0.000 0.053 0.709 0.365 2.188 4.417 1.704 0.380 2.085 Comparisons 040 - 045 Average 0.024 0.005 0.007 0.037 0.047 0.006 0.370 1.604 1.754 0.737 0.918 1.881 1.274 0.972 1.951 Std Dev 0.006 0.010 0.004 0.018 0.000 0.053 0.740 0.358 2.150 4.317 1.707 0.399 2.111 Comparisons 040 - 046 Average 0.024 0.005 0.007 0.037 0.045 0.006 0.370 1.608 1.754 0.739 0.917 1.858 1.260 0.972 1.955 Std Dev 0.006 0.010 0.004 0.018 0.000 0.052 0.746 0.355 2.147 4.317 1.710 0.397 2.122 Comparisons 040 - 047 Average 0.024 0.004 0.007 0.028 0.009 0.006 0.363 1.699 1.761 0.798 0.881 1.465 0.947 0.964 2.069 Std Dev 0.006 0.010 0.004 0.018 0.000 0.033 0.888 0.270 2.132 4.322 1.749 0.336 2.344 Appendix A Table A.32: The Calculated Energies for Selected M-N and M-O Bond Lengths M-O M-N E 2.000 2.000 25.368 2.000 2.100 22.964 2.000 2.200 21.464 2.000 2.300 20.837 2.000 2.400 21.038 2.000 2.500 22.017 2.000 2.600 23.722 2.100 2.000 24.676 2.100 2.100 22.302 2.100 2.200 20.827 2.100 2.300 20.219 2.100 2.400 20.434 2.100 2.500 21.419 2.100 2.600 23.121 2.200 2.000 24.237 2.200 2.100 21.885 2.200 2.200 20.429 2.200 2.300 19.835 2.200 2.400 20.058 2.200 2.500 21.043 2.200 2.600 22.736 2.300 2.000 24.054 2.300 2.100 21.718 2.300 2.200 20.274 2.300 2.300 19.688 2.300 2.400 19.913 2.300 2.500 20.893 2.300 2.600 22.573 2.400 2.000 24.132 2.400 2.100 21.807 2.400 2.200 20.368 2.400 2.300 19.784 2.400 2.400 20.004 2.400 2.500 20.972 2.400 2.600 22.633 2.500 2.000 24.477 2.500 2.100 22.155 40 Appendix A 2.500 2.200 20.716 2.500 2.300 20.126 2.500 2.400 20.336 2.500 2.500 21.287 2.500 2.600 22.922 2.600 2.000 25.093 2.600 2.100 22.767 2.600 2.200 21.322 2.600 2.300 20.721 2.600 2.400 20.913 2.600 2.500 21.840 2.600 2.600 23.443 Figure A.1: The VISTA histogram of the Cd(II)?O(H)(C) bond length 41 Appendix A Figure A.2: The VISTA histogram of the Cd(II) ?O(C) bond length Figure A.3: The VISTA histogram of the Cd(II) ?N(H)(C)(C) bond length 42 Appendix A Figure A.4: The VISTA histogram of the Cd(II) ?Cl bond length Figure A.5: The VISTA histogram of the N?Cd(II) ?N bond angle 43 Appendix A Figure A.6: The VISTA histogram of the N?Cd(II) ?O bond angle Figure A.7: The VISTA histogram of the Cl?Cd(II) ?Cl bond angle 44 Appendix A 45 Figure A.8: The VISTA histogram of the Cl?Cd(II) ?O(H)(R) bond angle Figure A.9: The VISTA histogram of the Cl?Cd(II) ?N(H)(R) bond angle Appendix B Appendix B ? NMR Data All NMR data was generated in the manner described in Chapter 2. Figure B.1: The 1H NMR of Cy2-en (Sample 1) 1 Appendix B Figure B.2: The 13C NMR of Cy2-en (Sample 1) Figure B.3: The 1H NMR of Cy2-en (Sample 2) 2 Appendix B Figure B.4: The 13C NMR of Cy2-en (Sample 2) Figure B.5: The 1H NMR of Cy2-en (Sample 3) 3 Appendix B Figure B.6: The 13C NMR of Cy2-en (Sample 3) Figure B.7: The 1H NMR of Cy2-tn (Sample 1) 4 Appendix B Figure B.8: The 13C NMR of Cy2-tn (Sample 1) Figure B.9: The 1H NMR of Cy2-tn (Sample 2) 5 Appendix B Figure B.10: The 13C NMR of Cy2-tn (Sample 2) Figure B.11: The 1H NMR of Cy2-dien (Sample 1) 6 Appendix B Figure B.12: The 13C NMR of Cy2-dien (Sample 1) Figure B.13: The 1H NMR of Cy2-dien (Sample 2) 7 Appendix B Figure B.14: The 13C NMR of Cy2-dien (Sample 2) Figure B.15: The 1H NMR of Cy2-Otn (Sample 1) 8 Appendix B Figure B.16: The 13C NMR of Cy2-Otn (Sample 1) Figure B.17: The 1H NMR of Cy2-Otn (Sample 2) 9 Appendix B Figure B.18: The 13C NMR of Cy2-Otn (Sample 2) Figure B.19: The 1H NMR of Cy2-Otn (Sample 3) 10 Appendix B Figure B.20: The 13C NMR of Cy2-Otn (Sample 3) Figure B.21: The 1H NMR of the Imidazolinium Salt 11 Appendix B 12 Figure B.22: The 13C NMR of the Imidazolinium Salt Figure B.23: The 1H NMR of the Protonated Cy2-en Chloride Salt Appendix C Appendix C ? IR Data All IR data was generated in the manner described in Chapter 2. Figure C.1: The IR of Cy2-en (Sample 1) 1 Appendix C Figure C.2: The IR of Cy2-en (Sample 2) Figure C.3: The IR of Cy2-en (Sample 3) 2 Appendix C Figure C.4: The IR of Cy2-tn (Sample 1) Figure C.5: The IR of Cy2-tn (Sample 2) 3 Appendix C Figure C.6: The IR of Cy2-dien (Sample 1) Figure C.7: The IR of Cy2-dien (Sample 2) 4 Appendix C Figure C.8: The IR of Cy2-Otn (Sample 1) Figure C.9: The IR of Cy2-Otn (Sample 2) 5 Appendix C Figure C.10: The IR of Cy2-Otn (Sample 3) Figure C.11: The IR of the Imidazolinium Salt from the Attempted Cy2-en/Pb(II) Reaction (Method 1) 6 Appendix C Figure C.12: The IR of the Attempted Cy2-en/Pb(II) Reaction (Method 2) Figure C.13: The IR of the Attempted Cy2-en/Pb(II) Reaction (Method 3) 7 Appendix C Figure C.14: The IR of the Successful Cy2-en/Pb(II) Complex (Method 5) Figure C.15: The IR of the Attempted Cy2-tn/Pb(II) Complex 8 Appendix C Figure C.16: The IR of the Cy2-dien/Pb(II) Complex Figure C.17: The IR of the Cy2-Otn/Pb(II) Complex 9 Appendix C Figure C.18: The IR of the BHEEN/Pb(II) Complex Figure C.19: The IR of the Cy2-en/Cd(II) Complex 10 Appendix C Figure C.20: The IR of the Cy2-tn/Cd(II) Complex Figure C.21: The IR of the Cy2-dien/Cd(II) Complex 11 Appendix C Figure C.22: The IR of the Cy2-Otn/Cd(II) Complex Figure C.23: The IR of the BHEEN/Cd(II) Complex 12 Appendix C Figure C.24: The IR of the Cy2-en/Ni(II) Complex Figure C.25: The IR of the Cy2-Otn/Ni(II) Complex 13 Appendix C Figure C.26: The IR of the BHEEN/Ni(II) Complex Figure C.27: The IR of the Cy2-en/Zn(II) Complex 14 Appendix C Figure C.28: The IR of the Cy2-Otn/Zn(II) Complex Figure C.29: The IR of the BHEEN/Zn(II) Complex 15 Appendix C 16 Figure C.30: The IR BHEEN (Sigma) Figure C.31: The IR the Zwitterion 2 Appendix D Appendix D ? MS Data All MS data was generated in the manner described in Chapter 2. Figure D.1: The APCI Spectrum of Cy2-en (Sample 1) 100 200 300 400 500 600 700 800 900 1000 m/z 0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80 90 100 R el at iv e A bu nd an ce 233.29 219.25 355.33 609.51 467.32193.16 253.29 187.11 519.41 263.34 773.47694.55535.53 159.20 789.52 873.06 985.95124.05 257.25 159.23 269.27 521.42355.44 566.46 785.56659.29 946.60860.78 NL: 9.15E1 SAR001#1-10 RT: 0.02-0.18 AV: 5 SB: 50 1.00-3.00 F: ITMS - c APCI corona Full ms [50.00-1000.00] NL: 5.52E5 SAR001#1-10 RT: 0.04-0.20 AV: 5 SB: 49 1.00-3.00 F: ITMS + c APCI corona Full ms [50.00-1000.00] SAR001 # 1-9 RT: 0.04-0.16 AV: 4 NL: 6.75E5 F: ITMS + c APCI corona Full ms [50.00-1000.00] 1 Appendix D Figure D.2: The ESI+ Spectrum of Cy 2-en (Sample 2) SAR020q # 2-13 RT: 0.03-0.18 AV: 6 SB: 97 1.01-4.01 NL: 1.62E6 F: ITMS + c ESI Full ms [50.00-700.00] 50 100 150 200 250 300 350 400 450 500 550 600 650 700 m/z 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 257 258 R el at iv e A bu nd an ce 279 142 438 339 280 438 577340 391 558143124 618239 479 536314 405 633 671183 221 687116 Figure D.3: The APCI Spectrum of Cy2-en (Sample 3) 100 200 300 400 500 600 700 m/z 0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80 90 100 R el at iv e A bu nd an ce 368.342 355.352 695.397535.519401.353 653.286 421.353 592.608492.438 325.320239.081165.179117.175 257.328 235.331142.291 269.324 521.497461.994355.419 627.677 684.185106.233 NL: 1.61E2 SAR036_apci#9-37 RT: 0.21-0.80 AV: 15 SB: 63 1.01-4.00 F: ITMS - c APCI corona Full ms [50.00-700.00] NL: 2.18E6 SAR036_apci#9-37 RT: 0.23-0.78 AV: 14 SB: 63 1.01-4.00 F: ITMS + c APCI corona Full ms [50.00-700.00] 2 Appendix D Figure D.4: The APCI Spectrum of Cy2-tn (Sample 1) 100 200 300 400 500 600 700 800 900 1000 m/z 0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80 90 100 R el at iv e A bu nd an ce 193.19 547.40 247.28 404.12 645.67277.30161.18 511.40 743.74637.54147.05 783.42 923.48 271.31 369.35154.21 549.45251.33 467.47 647.64 692.41 827.89 925.92 NL: 2.74E2 SAR002#1-10 RT: 0.02-0.18 AV: 5 F: ITMS - c APCI corona Full ms [50.00-1000.00] NL: 5.38E5 SAR002#1-10 RT: 0.04-0.21 AV: 5 F: ITMS + c APCI corona Full ms [50.00-1000.00] Figure D.5: The ESI Spectrum of Cy2-tn (Sample 2) 100 200 300 400 500 600 700 m/z 0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80 90 100 R el at iv e A bu nd an ce 367.33 269.28 249.00 270.32 384.97 520.92465.35 653.45 623.18325.20220.27155.08113.04 271.32 369.40272.34 293.31 370.42 549.55156.28 467.51 692.27594.53253.41128.16 NL: 2.88E3 SAR009_ESI#1-13 RT: 0.02-0.19 AV: 7 SB: 97 1.00-4.01 F: ITMS - c ESI Full ms [50.00-700.00] NL: 3.82E6 SAR009_ESI#1-13 RT: 0.03-0.18 AV: 6 SB: 97 1.00-4.01 F: ITMS + c ESI Full ms [50.00-700.00] 3 Appendix D Figure D.6: The APCI Spectrum of Cy2-dien (Sample 1) 100 200 300 400 500 600 700 800 900 1000 m/z 0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80 90 100 R el at iv e A bu nd an ce 605.52 193.18 219.28 298.41 443.18 495.26 695.63187.26 780.74 847.53 910.55 300.34 257.29 312.30 607.50398.40128.19 494.20 727.76 901.54817.50 976.47 NL: 5.54E2 SAR003#1-10 RT: 0.02-0.18 AV: 5 F: ITMS - c APCI corona Full ms [50.00-1000.00] NL: 4.74E5 SAR003#1-10 RT: 0.04-0.21 AV: 5 F: ITMS + c APCI corona Full ms [50.00-1000.00] Figure D.7: The ESI Spectrum of Cy2-dien (Sample 2) 100 200 300 400 500 600 700 m/z 0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80 90 100 R el at iv e A bu nd an ce 298.26 396.36 299.33249.03 494.46 397.41 320.28 520.92 653.36464.32 562.49155.06 227.39113.11 300.38 322.34 420.44 323.38257.36 421.47185.33 496.54142.26 629.63 674.47537.51 NL: 9.37E3 SAR010_ESI#1-13 RT: 0.02-0.20 AV: 7 SB: 98 1.00-4.01 F: ITMS - c ESI Full ms [50.00-700.00] NL: 4.46E6 SAR010_ESI#1-13 RT: 0.03-0.18 AV: 6 SB: 98 1.00-4.01 F: ITMS + c ESI Full ms [50.00-700.00] 4 Appendix D Figure D.8: The APCI Spectrum of Cy2-Otn (Sample 1) 100 200 300 400 500 600 m/z 0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80 90 100 R el at iv e A bu nd an ce 615.349 385.375 339.380 587.570393.302 451.256 293.339 517.443 277.073140.155 287.341 189.289 295.321 385.362256.349 617.428551.658495.411128.277 NL: 6.26E1 SAR022#1-9 RT: 0.02-0.20 AV: 5 SB: 39 1.00-2.87 F: ITMS - c APCI corona Full ms [50.00-650.00] NL: 4.01E4 SAR022#1-9 RT: 0.04-0.18 AV: 4 SB: 40 1.00-2.87 F: ITMS + c APCI corona Full ms [50.00-650.00] Figure D.9: The APCI Spectrum of Cy2-Otn (Sample 2) 100 200 300 400 500 600 700 m/z 0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80 90 100 R el at iv e A bu nd an ce 345.282 411.413 579.543 406.380 495.446 471.423 555.477 597.497 653.292 285.325 239.258165.098124.109 287.352 269.445189.309 315.394 413.405128.268 471.501 536.124 581.688 658.552 NL: 1.37E2 SAR025_apci#9-37 RT: 0.21-0.80 AV: 15 SB: 62 1.01-3.99 F: ITMS - c APCI corona Full ms [50.00-700.00] NL: 3.15E6 SAR025_apci#9-37 RT: 0.23-0.78 AV: 14 SB: 63 1.01-3.99 F: ITMS + c APCI corona Full ms [50.00-700.00] 5 Appendix D Figure D.10: The ESI Spectrum of Cy2-Otn (Sample 3) SAR038 # 16-62 RT: 0.30-1.00 AV: 24 SB: 94 1.00-4.00 NL: 7.31E5 F: ITMS + c ESI Full ms [50.00-700.00] 50 100 150 200 250 300 350 400 450 500 550 600 650 700 m/z 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 287.32 288.32 R el at iv e A bu nd an ce 603.53172.24 581.56310.36 604.52269.34154.25 173.25128.23 370.25 697.42505.43483.46 553.45407.37 Figure D.11: The APCI Spectrum of the Imidazolinium Salt from the Attempted Cy2- en/Pb(II) Reaction (Method 1) 50 100 150 200 250 300 350 400 450 500 550 600 m/z 0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80 90 100 R el at iv e A bu nd an ce 339.283 330.106 382.356 311.224 391.278 515.507459.269 549.447255.378147.180104.193 267.291 285.306 142.206 471.254239.369 379.361 572.280110.257 NL: 4.73E2 SAR007#1-9 RT: 0.02-0.19 AV: 5 SB: 43 1.01-3.00 F: ITMS - c APCI corona Full ms [50.00-600.00] NL: 1.09E6 SAR007#1-9 RT: 0.04-0.17 AV: 4 SB: 43 1.01-3.00 F: ITMS + c APCI corona Full ms [50.00-600.00] 6 Appendix D Figure D.12: The APCI Spectrum of the Attempted Cy2-en/Pb(II) Reaction (Method 2) 100 200 300 400 500 600 700 800 900 1000 m/z 0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80 90 100 R el at iv e A bu nd an ce 193.16 127.07 219.28 373.43267.01 607.42385.27 652.87 745.02508.69 870.80401.44 920.94 257.24 177.17 128.26 299.06 607.39463.00411.28 661.54 765.53 823.13 944.46 NL: 1.13E2 SAR013_1#1-10 RT: 0.02-0.18 AV: 5 SB: 50 1.00-3.00 F: ITMS - c APCI corona Full ms [50.00-1000.00] NL: 2.62E3 SAR013_1#1-10 RT: 0.04-0.21 AV: 5 SB: 49 1.00-3.00 F: ITMS + c APCI corona Full ms [50.00-1000.00] Figure D.13: The APCI Spectrum of the Attempted Cy2-en/Pb(II) Reaction (Method 3) 100 200 300 400 500 600 700 800 900 1000 m/z 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 0 257.26 159.22 265.31 269.30 463.33 599.13 705.40 796.74 860.85 977.27 NL: 4.38E4 SAR014_0#1-10 RT: 0.04-0.21 AV: 5 SB: 49 1.00-3.00 F: ITMS + c APCI corona Full ms [50.00-1000.00] 7 Appendix D Figure D.14: The APCI Spectrum of the Attempted Cy2-en/Pb(II) Reaction (Method 4) 100 200 300 400 500 600 700 800 900 1000 m/z 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 0 257.27 237.30128.17 269.31 463.26 585.21 781.56355.37 727.21 923.48 NL: 1.99E5 SAR015_0#1-10 RT: 0.04-0.21 AV: 5 SB: 49 1.00-3.00 F: ITMS + c APCI corona Full ms [50.00-1000.00] Figure D.15: The APCI Spectrum of the Successful Cy2-en/Pb(II) Complex (Method 5) 100 200 300 400 500 600 700 800 900 1000 m/z 0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80 90 100 R el at iv e A bu nd an ce 233.24 243.16225.20 354.24 609.49 653.08145.18 371.26 565.32 846.66 955.37 257.31 237.23 269.27159.29 463.30 521.39 741.14588.28355.30 784.49 925.39 NL: 2.94E2 SAR008_2#1-10 RT: 0.02-0.18 AV: 5 SB: 50 1.00-3.00 F: ITMS - c APCI corona Full ms [50.00-1000.00] NL: 9.22E5 SAR008_2#1-10 RT: 0.04-0.20 AV: 5 SB: 49 1.00-3.00 F: ITMS + c APCI corona Full ms [50.00-1000.00] 8 Appendix D Figure D.16: The APCI Spectrum of the Attempted Cy2-tn/Pb(II) Complex 100 200 300 400 500 600 700 800 900 1000 m/z 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 0 271.32 300.35 173.32 214.27 163.20 599.32551.47143.29 351.39 662.14403.44 910.15 951.88856.84 NL: 3.64E3 SAR011_1#1-10 RT: 0.04-0.21 AV: 5 SB: 49 1.00-3.00 F: ITMS + c APCI corona Full ms [50.00-1000.00] Figure D.17: The APCI Spectrum of the Cy2-dien/Pb(II) Complex SAR012_apci2 # 9-35 RT: 0.23-0.78 AV: 13 SB: 63 1.01-4.00 NL: 7.96E5 F: ITMS + c APCI corona Full ms [50.00-700.00] 50 100 150 200 250 300 350 400 450 500 550 600 650 700 m/z 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 300 301 R el at iv e A bu nd an ce 398 257 399302 322276185 496 608356142 454242 536224 593 653124 672 9 Appendix D Figure D.18: The APCI Spectrum of the BHEEN/Pb(II) Complex 100 200 300 400 500 600 700 m/z 0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80 90 100 R el at iv e A bu nd an ce 695.416 653.192 373.443 521.179 565.182409.446 339.247265.125191.145117.070 462.030 445.151 536.089 371.181 610.195 519.043282.405237.264 684.218149.173107.125 NL: 4.99E1 SAR031_apci#9-34 RT: 0.21-0.77 AV: 13 SB: 63 1.01-4.01 F: ITMS - c APCI corona Full ms [50.00-700.00] NL: 2.81E4 SAR031_apci#9-34 RT: 0.23-0.79 AV: 13 SB: 62 1.01-4.01 F: ITMS + c APCI corona Full ms [50.00-700.00] Figure D.19: The APCI Spectrum of the Cy2-en/Cd(II) Complex 100 200 300 400 500 600 700 800 900 1000 m/z 0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80 90 100 R el at iv e A bu nd an ce 193.15 219.19 233.29 344.13 346.22317.42159.18 429.45 741.25668.87569.26 782.54 927.58 257.27 265.29128.25 237.26 338.39 521.35 566.62 845.13657.97 900.98741.74 NL: 3.62E2 SAR016_1_07090516004 6#1-10 RT: 0.02-0.18 AV: 5 F: ITMS - c APCI corona Full ms [50.00-1000.00] NL: 2.26E5 SAR016_1_07090516004 6#1-10 RT: 0.04-0.21 AV: 5 F: ITMS + c APCI corona Full ms [50.00-1000.00] 10 Appendix D Figure D.20: The APCI Spectrum of the Cy2-tn/Cd(II) Complex 100 200 300 400 500 600 700 m/z 0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80 90 100 R el at iv e A bu nd an ce 653.227 695.397593.258 266.977 521.225 439.438 291.032 465.477 565.179242.941 397.451 357.166 337.140220.986165.114 271.349 156.279 251.347 369.392283.359 445.109 536.090116.256 641.654 NL: 3.07E1 SAR018_1_apci#9-37 RT: 0.21-0.80 AV: 15 SB: 63 1.00-4.01 F: ITMS - c APCI corona Full ms [50.00-700.00] NL: 2.19E6 SAR018_1_apci#9-37 RT: 0.23-0.79 AV: 14 SB: 64 1.00-4.01 F: ITMS + c APCI corona Full ms [50.00-700.00] Figure D.21: The ESI Spectrum of the Cy2-tn/Cd(II) Complex 100 200 300 400 500 600 700 m/z 0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80 90 100 R el at iv e A bu nd an ce 291.05 267.00 265.02 242.97 293.09240.97 345.07 593.16239.90 520.87 673.12374.50 402.78 524.86112.96 215.87 271.34 272.37 156.24 273.43 443.28369.45 577.29253.36 549.60128.24 663.67 NL: 2.16E2 SAR018_1#18-66 RT: 0.31-0.98 AV: 24 SB: 99 0.99-4.00 F: ITMS - c ESI Full ms [50.00-700.00] NL: 1.13E6 SAR018_1#18-66 RT: 0.30-0.99 AV: 25 SB: 99 0.99-4.00 F: ITMS + c ESI Full ms [50.00-700.00] 11 Appendix D Figure D.22: The APCI Spectrum of the Cy2-dien/Cd(II) Complex 100 200 300 400 500 600 700 m/z 0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80 90 100 R el at iv e A bu nd an ce 605.580 396.437 449.348 653.155 373.400 494.561 565.407 355.363 298.432 141.100 267.065 300.390 257.341 398.451312.408 462.016185.337 536.110142.300 610.190 684.175 NL: 6.77E1 SAR019_apci#9-37 RT: 0.21-0.80 AV: 15 SB: 63 1.00-4.01 F: ITMS - c APCI corona Full ms [50.00-700.00] NL: 1.94E6 SAR019_apci#9-37 RT: 0.23-0.79 AV: 14 SB: 64 1.00-4.01 F: ITMS + c APCI corona Full ms [50.00-700.00] Figure D.23: The APCI Spectrum of the Cy2-Otn/Cd(II) Complex SAR028 # 9-35 RT: 0.23-0.78 AV: 13 SB: 65 1.00-4.01 NL: 1.09E6 F: ITMS + c APCI corona Full ms [50.00-700.00] 50 100 150 200 250 300 350 400 450 500 550 600 650 700 m/z 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 287.352 257.342 299.343 R el at iv e A bu nd an ce 189.275 435.273341.353128.210 536.111505.525 581.391 686.277627.724 12 Appendix D Figure D.24: The APCI Spectrum of the BHEEN/Cd(II) Complex SAR041 # 16-62 RT: 0.30-1.00 AV: 24 SB: 82 1.00-3.99 NL: 1.72E4 F: ITMS + c ESI Full ms [50.00-700.00] 50 100 150 200 250 300 350 400 450 500 550 600 650 700 m/z 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 297.09 295.11 259.13 R el at iv e A bu nd an ce 299.10129.21 258.14 257.11 591.07 555.11 519.13321.17 409.25 595.06516.14 406.25 627.01514.16323.21127.21 149.22 411.27253.17 685.48403.04205.18125.22 Figure D.25: The APCI Spectrum of the Cy2-en/Ni(II) Complex SAR040 # 9-39 RT: 0.23-0.79 AV: 15 SB: 65 1.01-4.00 NL: 1.01E6 F: ITMS + c APCI corona Full ms [50.00-700.00] 50 100 150 200 250 300 350 400 450 500 550 600 650 700 m/z 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 257.337 267.289 R el at iv e A bu nd an ce 349.292233.332 663.385159.290 373.252 569.394451.442 497.452116.262 13 Appendix D Figure D.26: The APCI Spectrum of the Cy2-Otn/Ni(II) Complex SAR037 # 9-36 RT: 0.23-0.80 AV: 14 SB: 63 1.01-4.00 NL: 8.96E5 F: ITMS + c APCI corona Full ms [50.00-700.00] 50 100 150 200 250 300 350 400 450 500 550 600 650 700 m/z 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 287.368 299.371 R el at iv e A bu nd an ce 189.376 229.336 343.286116.278 403.122 536.115462.006 685.442610.156 Figure D.27: The APCI Spectrum of the BHEEN/Ni(II) Complex SAR039 # 9-35 RT: 0.23-0.78 AV: 13 SB: 63 0.99-4.00 NL: 2.71E4 F: ITMS + c APCI corona Full ms [50.00-700.00] 50 100 150 200 250 300 350 400 450 500 550 600 650 700 m/z 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 149.281 353.368 189.227 241.239 447.265287.422 389.248205.225 R el at iv e A bu nd an ce 483.162 115.238 345.224 679.085651.196105.233 505.041409.319 541.121 14 Appendix D Figure D.28: The ESI Spectrum of the Cy2-en/Zn(II) Complex 100 200 300 400 500 600 700 m/z 0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80 90 100 R el at iv e A bu nd an ce 241.07 506.97 491.03 243.04 508.98 563.06 588.84489.04 590.94487.01245.09 511.00484.92 219.01 480.91 641.04324.98 381.01217.07 478.91 688.86321.02168.98 411.04 113.11 319.25 321.27 257.32 323.27 379.21 381.22 355.25 639.45258.36 677.37142.25 575.45384.28 505.23289.25239.37110.21 NL: 2.20E2 SAR023#18-66 RT: 0.32-0.98 AV: 24 SB: 100 1.00-3.99 F: ITMS - c ESI Full ms [50.00-700.00] NL: 3.51E5 SAR023#18-66 RT: 0.30-1.00 AV: 25 SB: 101 1.00-3.99 F: ITMS + c ESI Full ms [50.00-700.00] Figure D.29: The APCI Spectrum of the Cy2-Otn/Zn(II) Complex SAR045_080707105446 # 2 RT: 0.02 AV: 1 SB: 24 0.05-0.23 , 0.05-0.23 NL: 8.63E3 T: ITMS + c ESI Full ms [200.00-1000.00] 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 1000 m/z 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 R el at iv e A bu nd an ce 287.30 219.27 299.27243.23 409.12 537.17341.35 593.79463.09 513.28 612.30 685.08 741.06 760.50 15 Appendix D 16 Figure D.30: The APCI Spectrum of the BHEEN/Zn(II) Complex SAR048b_080707105446 # 5 RT: 0.06 AV: 1 SB: 24 0.06-0.22 , 0.06-0.22 NL: 3.74E5 T: ITMS + c ESI Full ms [50.00-800.00] 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 m/z 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 R el at iv e A bu nd an ce 149.23 175.24 203.29 247.18145.30 536.15309.35 395.22367.56 461.28439.65 667.50501.11 594.77 Figure D.31: The APCI Spectrum of the Zwitterion 2 100 200 300 400 500 600 700 m/z 0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80 90 100 R el at iv e A bu nd an ce 345.282 285.356 695.460569.158373.482 521.076 113.144 277.286165.317 287.313 172.198 269.396 299.293128.237 371.110 536.046445.069 610.128 684.154 NL: 1.81E2 SAM_L1_APCI#13-40 RT: 0.31-0.89 AV: 14 SB: 42 2.00-4.00 F: ITMS - c APCI corona Full ms [50.00-700.00] NL: 4.74E5 SAM_L1_APCI#13-40 RT: 0.33-0.92 AV: 14 SB: 42 2.00-4.00 F: ITMS + c APCI corona Full ms [50.00-700.00] Appendix E Appendix E XRD Data Cy2-en Data Figure E.1: XRD structure of Cy2-en and the labelling scheme used Table E.1: Crystal data and structure refinement for 7m_al3_0s. Identification code 7m_al3_0s Empirical formula C32 H4 N4 O4 Formula weight 508.39 Temperature 293(2) K Wavelength 0.71069 ? Crystal system Monoclinic Space group P2(1)/c Unit cell dimensions a = 12.281(5) ? ? = 90?. b = 8.110(5) ? ? = 102.776(5)?. c = 7.123(5) ? ? = 90?. Volume 691.9(7) ?3 Z 1 Density (calculated) 1.220 Mg/m3 Absorption coefficient 0.084 mm-1 F(000) 256 Crystal size 0.42 x 0.38 x 0.10 mm3 Theta range for data collection 1.70 to 28.31?. 1 Appendix E Index ranges -16<=h<=16, -10<=k<=10, -9<=l<=9 Reflections collected 9394 Independent reflections 1721 [R(int) = 0.1057] Completeness to theta = 28.31? 99.7 % Absorption correction None Refinement method Full-matrix least-squares on F2 Data / restraints / parameters 1721 / 0 / 87 Goodness-of-fit on F2 1.038 Final R indices [I>2sigma(I)] R1 = 0.0584, wR2 = 0.1399 R indices (all data) R1 = 0.0784, wR2 = 0.1520 Largest diff. peak and hole 0.378 and -0.251 e.?-3 Table E.2: Atomic coordinates ( x 104) and equivalent isotropic displacement parameters (?2x 103) for 7m_al3_0s. U(eq) is defined as one third of the trace of the orthogonalized Uij tensor. x y z U(eq) C(1) 2939(1) 4047(2) 9017(2) 16(1) C(2) 1983(2) 4769(2) 9797(2) 23(1) C(3) 936(2) 5027(2) 8225(3) 28(1) C(4) 1193(2) 6074(2) 6600(2) 23(1) C(5) 2140(1) 5326(2) 5817(2) 20(1) C(6) 3186(1) 5119(2) 7405(2) 15(1) C(7) 4468(1) 5351(2) 5208(2) 18(1) O(1) 3913(1) 3906(1) 10509(2) 20(1) N(1) 4113(1) 4372(2) 6704(2) 16(1) Table E.3: Bond lengths [?] and angles [?] for 7m_al3_0s. C(1)-O(1) 1.418(2) C(1)-C(2) 1.522(2) C(1)-C(6) 1.523(2) C(1)-H(1A) 0.9800 C(2)-C(3) 1.521(3) C(2)-H(2A) 0.9700 C(2)-H(2B) 0.9700 C(3)-C(4) 1.524(2) C(3)-H(3A) 0.9700 C(3)-H(3B) 0.9700 C(4)-C(5) 1.523(2) C(4)-H(4A) 0.9700 2 Appendix E C(4)-H(4B) 0.9700 C(5)-C(6) 1.522(2) C(5)-H(5A) 0.9700 C(5)-H(5B) 0.9700 C(6)-N(1) 1.470(2) C(6)-H(6) 0.9800 C(7)-N(1) 1.471(2) C(7)-C(7)#1 1.514(3) C(7)-H(7A) 0.9700 C(7)-H(7B) 0.9700 O(1)-H(1O) 0.8200 N(1)-H(1N) 0.83(2) O(1)-C(1)-C(2) 110.37(13) O(1)-C(1)-C(6) 109.56(13) C(2)-C(1)-C(6) 110.77(13) O(1)-C(1)-H(1A) 108.7 C(2)-C(1)-H(1A) 108.7 C(6)-C(1)-H(1A) 108.7 C(3)-C(2)-C(1) 112.22(14) C(3)-C(2)-H(2A) 109.2 C(1)-C(2)-H(2A) 109.2 C(3)-C(2)-H(2B) 109.2 C(1)-C(2)-H(2B) 109.2 H(2A)-C(2)-H(2B) 107.9 C(2)-C(3)-C(4) 110.67(15) C(2)-C(3)-H(3A) 109.5 C(4)-C(3)-H(3A) 109.5 C(2)-C(3)-H(3B) 109.5 C(4)-C(3)-H(3B) 109.5 H(3A)-C(3)-H(3B) 108.1 C(5)-C(4)-C(3) 111.03(14) C(5)-C(4)-H(4A) 109.4 C(3)-C(4)-H(4A) 109.4 C(5)-C(4)-H(4B) 109.4 C(3)-C(4)-H(4B) 109.4 H(4A)-C(4)-H(4B) 108.0 C(4)-C(5)-C(6) 111.08(14) C(4)-C(5)-H(5A) 109.4 C(6)-C(5)-H(5A) 109.4 C(4)-C(5)-H(5B) 109.4 C(6)-C(5)-H(5B) 109.4 H(5A)-C(5)-H(5B) 108.0 N(1)-C(6)-C(5) 112.49(13) N(1)-C(6)-C(1) 108.63(13) C(5)-C(6)-C(1) 110.28(14) 3 Appendix E N(1)-C(6)-H(6) 108.4 C(5)-C(6)-H(6) 108.4 C(1)-C(6)-H(6) 108.4 N(1)-C(7)-C(7)#1 110.22(16) N(1)-C(7)-H(7A) 109.6 C(7)#1-C(7)-H(7A) 109.6 N(1)-C(7)-H(7B) 109.6 C(7)#1-C(7)-H(7B) 109.6 H(7A)-C(7)-H(7B) 108.1 C(1)-O(1)-H(1O) 109.5 C(6)-N(1)-C(7) 113.54(13) C(6)-N(1)-H(1N) 107.9(14) C(7)-N(1)-H(1N) 102.9(14) Symmetry transformations used to generate equivalent atoms: #1 -x+1,-y+1,-z+1 Table E.4: Anisotropic displacement parameters (?2x 103)for 7m_al3_0s. The anisotropic displacement factor exponent takes the form: -2p2[ h2a*2U11 + ... + 2 h k a* b* U12 ] U11 U22 U33 U23 U13 U12 C(1) 21(1) 14(1) 13(1) 1(1) 4(1) -1(1) C(2) 30(1) 24(1) 17(1) 3(1) 12(1) 2(1) C(3) 25(1) 33(1) 29(1) 9(1) 12(1) 3(1) C(4) 24(1) 22(1) 22(1) 2(1) 5(1) 2(1) C(5) 26(1) 19(1) 15(1) 1(1) 6(1) 2(1) C(6) 22(1) 11(1) 14(1) -1(1) 6(1) -1(1) C(7) 25(1) 16(1) 15(1) 2(1) 7(1) -1(1) O(1) 28(1) 17(1) 14(1) 3(1) 2(1) -1(1) N(1) 21(1) 15(1) 11(1) 0(1) 5(1) 0(1) Table E.5: Torsion angles [?] for 7m_al3_0s. O(1)-C(1)-C(2)-C(3) 177.01(13) C(6)-C(1)-C(2)-C(3) 55.48(19) C(1)-C(2)-C(3)-C(4) -54.6(2) C(2)-C(3)-C(4)-C(5) 55.0(2) C(3)-C(4)-C(5)-C(6) -57.13(19) C(4)-C(5)-C(6)-N(1) 179.04(13) C(4)-C(5)-C(6)-C(1) 57.59(17) O(1)-C(1)-C(6)-N(1) 57.96(16) C(2)-C(1)-C(6)-N(1) 179.96(13) O(1)-C(1)-C(6)-C(5) -178.33(12) 4 Appendix E C(2)-C(1)-C(6)-C(5) -56.32(17) C(5)-C(6)-N(1)-C(7) 60.74(18) C(1)-C(6)-N(1)-C(7) -176.88(13) C(7)#1-C(7)-N(1)-C(6) 171.04(16) Symmetry transformations used to generate equivalent atoms: #1 -x+1,-y+1,-z+1 Table E.6: Hydrogen bonds for 7m_al3_0s [? and ?]. D-H...A d(D-H) d(H...A) d(D...A) <(DHA) O(1)-H(1O)...N(1)#2 0.82 1.97 2.785(2) 175.1 Symmetry transformations used to generate equivalent atoms: #1 -x+1,-y+1,-z+1 #2 x,-y+1/2,z+1/2 Figure E.2: XRD structure of the protonated Cy2-en and the labelling scheme used Table E.7: Crystal data and structure refinement for 7m_al6_0s. Identification code 7m_al6_0s Empirical formula C14 H30 Cl2 N2 O2 Formula weight 329.30 5 Appendix E Temperature 293(2) K Wavelength 0.71073 ? Crystal system Triclinic Space group P-1 Unit cell dimensions a = 5.8557(3) ? ? = 97.885(3)?. b = 6.9089(3) ? ? = 98.174(4)?. c = 11.1223(7) ? ? = 107.415(3)?. Volume 417.21(4) ?3 Z 1 Density (calculated) 1.311 Mg/m3 Absorption coefficient 0.393 mm-1 F(000) 178 Crystal size 0.35 x 0.31 x 0.07 mm3 Theta range for data collection 1.88 to 25.49?. Index ranges -7<=h<=7, -8<=k<=8, -13<=l<=12 Reflections collected 5128 Independent reflections 1533 [R(int) = 0.0476] Completeness to theta = 25.49? 98.8 % Absorption correction Multiscan Max. and min. transmission 0.9730 and 0.8747 Refinement method Full-matrix least-squares on F2 Data / restraints / parameters 1533 / 0 / 92 Goodness-of-fit on F2 1.306 Final R indices [I>2sigma(I)] R1 = 0.0586, wR2 = 0.1699 R indices (all data) R1 = 0.0615, wR2 = 0.1708 Largest diff. peak and hole 0.713 and -0.334 e.?-3 Table E.8: Atomic coordinates ( x 104) and equivalent isotropic displacement parameters (?2x 103) for 7m_al6_0s. U(eq) is defined as one third of the trace of the orthogonalized Uij tensor. x y z U(eq) C(1) 3106(9) 1363(7) 2173(4) 31(1) C(2) 2827(10) 284(8) 3266(4) 38(1) C(3) 3016(11) 1793(8) 4425(5) 45(1) C(4) 1127(12) 2868(9) 4243(5) 50(1) C(5) 1329(10) 3933(8) 3134(4) 37(1) C(6) 1211(8) 2433(6) 1975(4) 26(1) C(7) -182(8) 4604(7) 595(4) 27(1) Cl(1) 6262(2) 7355(2) 1634(1) 35(1) N(1) 1609(7) 3526(5) 909(3) 24(1) O(1) 2792(8) -28(6) 1035(3) 47(1) 6 Appendix E Table E.9: Bond lengths [?] and angles [?] for 7m_al6_0s. C(1)-O(1) 1.433(5) C(1)-C(2) 1.514(6) C(1)-C(6) 1.514(6) C(1)-H(1) 0.9800 C(2)-C(3) 1.510(7) C(2)-H(2A) 0.9700 C(2)-H(2B) 0.9700 C(3)-C(4) 1.512(8) C(3)-H(3A) 0.9700 C(3)-H(3B) 0.9700 C(4)-C(5) 1.521(7) C(4)-H(4A) 0.9700 C(4)-H(4B) 0.9700 C(5)-C(6) 1.518(6) C(5)-H(5A) 0.9700 C(5)-H(5B) 0.9700 C(6)-N(1) 1.500(5) C(6)-H(6) 0.9800 C(7)-N(1) 1.487(5) C(7)-C(7)#1 1.517(8) C(7)-H(7A) 0.9700 C(7)-H(7B) 0.9700 N(1)-H(1N1) 0.9000 N(1)-H(1N2) 0.9000 O(1)-H(1A) 0.8200 O(1)-C(1)-C(2) 113.0(4) O(1)-C(1)-C(6) 106.4(4) C(2)-C(1)-C(6) 110.6(4) O(1)-C(1)-H(1) 108.9 C(2)-C(1)-H(1) 108.9 C(6)-C(1)-H(1) 108.9 C(3)-C(2)-C(1) 110.9(4) C(3)-C(2)-H(2A) 109.5 C(1)-C(2)-H(2A) 109.5 C(3)-C(2)-H(2B) 109.5 C(1)-C(2)-H(2B) 109.5 H(2A)-C(2)-H(2B) 108.0 C(2)-C(3)-C(4) 110.9(4) C(2)-C(3)-H(3A) 109.5 C(4)-C(3)-H(3A) 109.5 C(2)-C(3)-H(3B) 109.5 C(4)-C(3)-H(3B) 109.5 H(3A)-C(3)-H(3B) 108.1 C(3)-C(4)-C(5) 111.4(4) 7 Appendix E C(3)-C(4)-H(4A) 109.3 C(5)-C(4)-H(4A) 109.3 C(3)-C(4)-H(4B) 109.3 C(5)-C(4)-H(4B) 109.3 H(4A)-C(4)-H(4B) 108.0 C(6)-C(5)-C(4) 111.2(4) C(6)-C(5)-H(5A) 109.4 C(4)-C(5)-H(5A) 109.4 C(6)-C(5)-H(5B) 109.4 C(4)-C(5)-H(5B) 109.4 H(5A)-C(5)-H(5B) 108.0 N(1)-C(6)-C(1) 108.6(3) N(1)-C(6)-C(5) 110.9(3) C(1)-C(6)-C(5) 111.4(4) N(1)-C(6)-H(6) 108.6 C(1)-C(6)-H(6) 108.6 C(5)-C(6)-H(6) 108.6 N(1)-C(7)-C(7)#1 109.3(4) N(1)-C(7)-H(7A) 109.8 C(7)#1-C(7)-H(7A) 109.8 N(1)-C(7)-H(7B) 109.8 C(7)#1-C(7)-H(7B) 109.8 H(7A)-C(7)-H(7B) 108.3 C(7)-N(1)-C(6) 114.1(3) C(7)-N(1)-H(1N1) 108.7 C(6)-N(1)-H(1N1) 108.7 C(7)-N(1)-H(1N2) 108.7 C(6)-N(1)-H(1N2) 108.7 H(1N1)-N(1)-H(1N2) 107.6 C(1)-O(1)-H(1A) 109.5 Symmetry transformations used to generate equivalent atoms: #1 -x,-y+1,-z Table E.10: Anisotropic displacement parameters (?2x 103) for 7m_al6_0s. The anisotropic displacement factor exponent takes the form: -2p2[ h2a*2U11 + ... + 2 h k a* b* U12 ] U11 U22 U33 U23 U13 U12 C(1) 37(3) 30(2) 29(2) 6(2) 1(2) 18(2) C(2) 49(3) 35(3) 35(3) 12(2) 1(2) 21(2) C(3) 63(4) 44(3) 32(3) 18(2) 7(2) 21(3) C(4) 73(4) 55(3) 39(3) 22(3) 26(3) 32(3) C(5) 53(3) 34(3) 34(3) 10(2) 15(2) 23(2) 8 Appendix E C(6) 30(2) 23(2) 27(2) 10(2) 6(2) 10(2) C(7) 28(2) 27(2) 30(2) 9(2) 5(2) 16(2) Cl(1) 28(1) 32(1) 46(1) 5(1) 10(1) 11(1) N(1) 31(2) 21(2) 24(2) 6(1) 5(2) 14(2) O(1) 74(3) 46(2) 36(2) 5(2) 5(2) 42(2) Table E.11: Torsion angles [?] for 7m_al6_0s. O(1)-C(1)-C(2)-C(3) -176.4(4) C(6)-C(1)-C(2)-C(3) -57.3(6) C(1)-C(2)-C(3)-C(4) 57.3(6) C(2)-C(3)-C(4)-C(5) -55.7(7) C(3)-C(4)-C(5)-C(6) 54.3(6) O(1)-C(1)-C(6)-N(1) -58.5(5) C(2)-C(1)-C(6)-N(1) 178.4(4) O(1)-C(1)-C(6)-C(5) 179.0(4) C(2)-C(1)-C(6)-C(5) 55.9(5) C(4)-C(5)-C(6)-N(1) -175.5(4) C(4)-C(5)-C(6)-C(1) -54.4(6) C(7)#1-C(7)-N(1)-C(6) -172.3(4) C(1)-C(6)-N(1)-C(7) 178.6(4) C(5)-C(6)-N(1)-C(7) -58.7(5) Symmetry transformations used to generate equivalent atoms: #1 -x,-y+1,-z Table E.12: Hydrogen bonds for 7m_al6_0s [? and ?]. D-H...A d(D-H) d(H...A) d(D...A) <(DHA) N(1)-H(1N1)...Cl(1) 0.90 2.22 3.090(4) 163.9 N(1)-H(1N2)...Cl(1)#2 0.90 2.60 3.303(4) 135.3 O(1)-H(1A)...Cl(1)#3 0.82 2.35 3.160(4) 168.4 Symmetry transformations used to generate equivalent atoms: #1 -x,-y+1,-z #2 -x+1,-y+1,-z #3 x,y-1,z 9 Appendix E Cy2-Otn Data Figure E.3: XRD structure of Cy2-Otn and the labelling scheme used Table E.13: Crystal data and structure refinement for 7m_al19_0s. Identification code 7m_al19_0s Empirical formula C30 H62 N4 O7 Formula weight 590.84 Temperature 293(2) K Wavelength 0.71073 ? Crystal system Triclinic Space group P-1 Unit cell dimensions a = 10.0830(2) ? ? = 104.5330(10)?. b = 10.6966(3) ? ? = 104.7020(10)?. c = 16.6006(4) ? ? = 90.5310(10)?. Volume 1671.31(7) ?3 Z 2 Density (calculated) 1.174 Mg/m3 Absorption coefficient 0.083 mm-1 F(000) 652 Crystal size 0.42 x 0.22 x 0.16 mm3 Theta range for data collection 1.31 to 28.00?. Index ranges -13<=h<=13, -14<=k<=14, -21<=l<=21 Reflections collected 29863 Independent reflections 8075 [R(int) = 0.0548] Completeness to theta = 28.00? 100.0 % Absorption correction None Max. and min. transmission 0.9869 and 0.9662 10 Appendix E Refinement method Full-matrix least-squares on F2 Data / restraints / parameters 8075 / 0 / 397 Goodness-of-fit on F2 1.002 Final R indices [I>2sigma(I)] R1 = 0.0504, wR2 = 0.1196 R indices (all data) R1 = 0.0868, wR2 = 0.1338 Largest diff. peak and hole 0.397 and -0.226 e.?-3 Table E.14: Atomic coordinates ( x 104) and equivalent isotropic displacement parameters (?2x 103) for 7m_al19_0s. U(eq) is defined as one third of the trace of the orthogonalized Uij tensor. x y z U(eq) C(1) -1447(2) 5680(2) 3207(1) 28(1) C(2) -2250(2) 6857(2) 3151(1) 36(1) C(3) -3660(2) 6681(2) 3294(1) 39(1) C(4) -4453(2) 5476(2) 2657(1) 38(1) C(5) -3657(2) 4283(2) 2714(1) 35(1) C(6) -2239(2) 4462(2) 2577(1) 26(1) C(7) -1984(2) 2142(2) 2045(1) 31(1) C(8) -955(2) 1119(2) 2019(1) 27(1) C(9) -1687(2) -116(2) 1390(1) 35(1) C(10) -1480(2) -2161(2) 432(1) 32(1) C(11) -2417(2) -3078(2) 647(1) 39(1) C(12) -3182(2) -4090(2) -169(1) 53(1) C(13) -2190(2) -4828(2) -608(1) 53(1) C(14) -1166(2) -3941(2) -776(1) 40(1) C(15) -452(2) -2906(2) 29(1) 35(1) N(1) -1419(1) 3353(1) 2684(1) 27(1) N(2) -774(1) -1126(1) 1195(1) 30(1) O(1) -150(1) 5846(1) 3029(1) 33(1) O(2) 165(1) 1554(1) 1754(1) 31(1) O(3) 496(1) -2064(1) -126(1) 40(1) C(16) 6725(2) 10880(2) 7888(1) 32(1) C(17) 5788(2) 11611(2) 8394(1) 38(1) C(18) 5927(2) 11229(2) 9231(1) 38(1) C(19) 5648(2) 9785(2) 9061(1) 32(1) C(20) 6552(2) 9050(2) 8527(1) 29(1) C(21) 6396(2) 9438(2) 7691(1) 27(1) C(22) 6691(2) 7409(2) 6722(1) 37(1) C(23) 7632(2) 6675(2) 6239(1) 33(1) C(24) 7059(2) 5297(2) 5791(1) 39(1) C(25) 7607(2) 3175(2) 5005(1) 27(1) C(26) 6897(2) 2411(2) 5459(1) 37(1) 11 Appendix E C(27) 6490(2) 1022(2) 4942(1) 45(1) C(28) 7688(2) 354(2) 4687(1) 53(1) C(29) 8351(2) 1109(2) 4207(1) 43(1) C(30) 8802(2) 2474(2) 4760(1) 29(1) N(3) 7290(1) 8712(1) 7198(1) 30(1) N(4) 8123(1) 4476(1) 5561(1) 28(1) O(4) 6596(1) 11252(1) 7111(1) 46(1) O(5) 7833(1) 7341(1) 5631(1) 42(1) O(6) 9534(1) 3217(1) 4382(1) 31(1) O(7) 9337(1) 11798(1) 7277(1) 70(1) Table E.15: Bond lengths [?] and angles [?] for 7m_al19_0s. C(1)-O(1) 1.4304(17) C(1)-C(2) 1.514(2) C(1)-C(6) 1.517(2) C(1)-H(1A) 0.9800 C(2)-C(3) 1.517(2) C(2)-H(2A) 0.9700 C(2)-H(2B) 0.9700 C(3)-C(4) 1.513(2) C(3)-H(3A) 0.9700 C(3)-H(3B) 0.9700 C(4)-C(5) 1.524(2) C(4)-H(4A) 0.9700 C(4)-H(4B) 0.9700 C(5)-C(6) 1.521(2) C(5)-H(5A) 0.9700 C(5)-H(5B) 0.9700 C(6)-N(1) 1.474(2) C(6)-H(6A) 0.9800 C(7)-N(1) 1.456(2) C(7)-C(8) 1.515(2) C(7)-H(7A) 0.9700 C(7)-H(7B) 0.9700 C(8)-O(2) 1.4250(17) C(8)-C(9) 1.509(2) C(8)-H(8A) 0.9800 C(9)-N(2) 1.455(2) C(9)-H(9A) 0.9700 C(9)-H(9B) 0.9700 C(10)-N(2) 1.470(2) C(10)-C(15) 1.503(2) C(10)-C(11) 1.520(2) C(10)-H(10A) 0.9800 12 Appendix E C(11)-C(12) 1.523(3) C(11)-H(11A) 0.9700 C(11)-H(11B) 0.9700 C(12)-C(13) 1.501(3) C(12)-H(12A) 0.9700 C(12)-H(12B) 0.9700 C(13)-C(14) 1.518(3) C(13)-H(13A) 0.9700 C(13)-H(13B) 0.9700 C(14)-C(15) 1.512(2) C(14)-H(14A) 0.9700 C(14)-H(14B) 0.9700 C(15)-O(3) 1.420(2) C(15)-H(15A) 0.9800 N(1)-H(1N) 0.848(17) N(2)-H(2N) 0.836(18) O(1)-H(1O) 0.8200 O(2)-H(2O) 0.8200 O(3)-H(3O) 0.8200 C(16)-O(4) 1.4184(18) C(16)-C(21) 1.510(2) C(16)-C(17) 1.516(2) C(16)-H(16A) 0.9800 C(17)-C(18) 1.518(2) C(17)-H(17A) 0.9700 C(17)-H(17B) 0.9700 C(18)-C(19) 1.509(2) C(18)-H(18A) 0.9700 C(18)-H(18B) 0.9700 C(19)-C(20) 1.519(2) C(19)-H(19A) 0.9700 C(19)-H(19B) 0.9700 C(20)-C(21) 1.518(2) C(20)-H(20A) 0.9700 C(20)-H(20B) 0.9700 C(21)-N(3) 1.468(2) C(21)-H(21A) 0.9800 C(22)-N(3) 1.456(2) C(22)-C(23) 1.498(2) C(22)-H(22A) 0.9700 C(22)-H(22B) 0.9700 C(23)-O(5) 1.424(2) C(23)-C(24) 1.508(2) C(23)-H(23A) 0.9800 C(24)-N(4) 1.458(2) C(24)-H(24A) 0.9700 13 Appendix E C(24)-H(24B) 0.9700 C(25)-N(4) 1.469(2) C(25)-C(30) 1.515(2) C(25)-C(26) 1.523(2) C(25)-H(25A) 0.9800 C(26)-C(27) 1.511(2) C(26)-H(26A) 0.9700 C(26)-H(26B) 0.9700 C(27)-C(28) 1.508(3) C(27)-H(27A) 0.9700 C(27)-H(27B) 0.9700 C(28)-C(29) 1.522(3) C(28)-H(28A) 0.9700 C(28)-H(28B) 0.9700 C(29)-C(30) 1.512(2) C(29)-H(29A) 0.9700 C(29)-H(29B) 0.9700 C(30)-O(6) 1.4293(17) C(30)-H(30A) 0.9800 N(3)-H(3N) 0.816(17) N(4)-H(4N) 0.794(17) O(4)-H(4O) 0.8200 O(5)-H(5O) 0.8200 O(6)-H(6O) 0.8200 O(7)-H(7O) 1.21(4) O(7)-H(8O) 1.074(12) O(1)-C(1)-C(2) 110.36(13) O(1)-C(1)-C(6) 109.18(12) C(2)-C(1)-C(6) 111.21(13) O(1)-C(1)-H(1A) 108.7 C(2)-C(1)-H(1A) 108.7 C(6)-C(1)-H(1A) 108.7 C(1)-C(2)-C(3) 111.50(14) C(1)-C(2)-H(2A) 109.3 C(3)-C(2)-H(2A) 109.3 C(1)-C(2)-H(2B) 109.3 C(3)-C(2)-H(2B) 109.3 H(2A)-C(2)-H(2B) 108.0 C(4)-C(3)-C(2) 110.52(14) C(4)-C(3)-H(3A) 109.5 C(2)-C(3)-H(3A) 109.5 C(4)-C(3)-H(3B) 109.5 C(2)-C(3)-H(3B) 109.5 H(3A)-C(3)-H(3B) 108.1 C(3)-C(4)-C(5) 111.07(14) 14 Appendix E C(3)-C(4)-H(4A) 109.4 C(5)-C(4)-H(4A) 109.4 C(3)-C(4)-H(4B) 109.4 C(5)-C(4)-H(4B) 109.4 H(4A)-C(4)-H(4B) 108.0 C(6)-C(5)-C(4) 111.00(14) C(6)-C(5)-H(5A) 109.4 C(4)-C(5)-H(5A) 109.4 C(6)-C(5)-H(5B) 109.4 C(4)-C(5)-H(5B) 109.4 H(5A)-C(5)-H(5B) 108.0 N(1)-C(6)-C(1) 108.28(12) N(1)-C(6)-C(5) 111.82(13) C(1)-C(6)-C(5) 110.96(13) N(1)-C(6)-H(6A) 108.6 C(1)-C(6)-H(6A) 108.6 C(5)-C(6)-H(6A) 108.6 N(1)-C(7)-C(8) 112.57(12) N(1)-C(7)-H(7A) 109.1 C(8)-C(7)-H(7A) 109.1 N(1)-C(7)-H(7B) 109.1 C(8)-C(7)-H(7B) 109.1 H(7A)-C(7)-H(7B) 107.8 O(2)-C(8)-C(9) 111.27(13) O(2)-C(8)-C(7) 108.91(13) C(9)-C(8)-C(7) 107.70(12) O(2)-C(8)-H(8A) 109.6 C(9)-C(8)-H(8A) 109.6 C(7)-C(8)-H(8A) 109.6 N(2)-C(9)-C(8) 113.71(13) N(2)-C(9)-H(9A) 108.8 C(8)-C(9)-H(9A) 108.8 N(2)-C(9)-H(9B) 108.8 C(8)-C(9)-H(9B) 108.8 H(9A)-C(9)-H(9B) 107.7 N(2)-C(10)-C(15) 110.39(13) N(2)-C(10)-C(11) 112.04(14) C(15)-C(10)-C(11) 109.98(14) N(2)-C(10)-H(10A) 108.1 C(15)-C(10)-H(10A) 108.1 C(11)-C(10)-H(10A) 108.1 C(10)-C(11)-C(12) 110.22(15) C(10)-C(11)-H(11A) 109.6 C(12)-C(11)-H(11A) 109.6 C(10)-C(11)-H(11B) 109.6 C(12)-C(11)-H(11B) 109.6 15 Appendix E H(11A)-C(11)-H(11B) 108.1 C(13)-C(12)-C(11) 110.74(16) C(13)-C(12)-H(12A) 109.5 C(11)-C(12)-H(12A) 109.5 C(13)-C(12)-H(12B) 109.5 C(11)-C(12)-H(12B) 109.5 H(12A)-C(12)-H(12B) 108.1 C(12)-C(13)-C(14) 112.32(16) C(12)-C(13)-H(13A) 109.1 C(14)-C(13)-H(13A) 109.1 C(12)-C(13)-H(13B) 109.1 C(14)-C(13)-H(13B) 109.1 H(13A)-C(13)-H(13B) 107.9 C(15)-C(14)-C(13) 112.13(15) C(15)-C(14)-H(14A) 109.2 C(13)-C(14)-H(14A) 109.2 C(15)-C(14)-H(14B) 109.2 C(13)-C(14)-H(14B) 109.2 H(14A)-C(14)-H(14B) 107.9 O(3)-C(15)-C(10) 111.23(14) O(3)-C(15)-C(14) 112.45(14) C(10)-C(15)-C(14) 110.92(14) O(3)-C(15)-H(15A) 107.3 C(10)-C(15)-H(15A) 107.3 C(14)-C(15)-H(15A) 107.3 C(7)-N(1)-C(6) 113.95(12) C(7)-N(1)-H(1N) 107.7(11) C(6)-N(1)-H(1N) 106.6(12) C(9)-N(2)-C(10) 110.72(12) C(9)-N(2)-H(2N) 104.0(12) C(10)-N(2)-H(2N) 104.8(12) C(1)-O(1)-H(1O) 109.5 C(8)-O(2)-H(2O) 109.5 C(15)-O(3)-H(3O) 109.5 O(4)-C(16)-C(21) 110.10(14) O(4)-C(16)-C(17) 110.60(13) C(21)-C(16)-C(17) 110.38(13) O(4)-C(16)-H(16A) 108.6 C(21)-C(16)-H(16A) 108.6 C(17)-C(16)-H(16A) 108.6 C(16)-C(17)-C(18) 111.04(14) C(16)-C(17)-H(17A) 109.4 C(18)-C(17)-H(17A) 109.4 C(16)-C(17)-H(17B) 109.4 C(18)-C(17)-H(17B) 109.4 H(17A)-C(17)-H(17B) 108.0 16 Appendix E C(19)-C(18)-C(17) 110.99(14) C(19)-C(18)-H(18A) 109.4 C(17)-C(18)-H(18A) 109.4 C(19)-C(18)-H(18B) 109.4 C(17)-C(18)-H(18B) 109.4 H(18A)-C(18)-H(18B) 108.0 C(18)-C(19)-C(20) 111.02(13) C(18)-C(19)-H(19A) 109.4 C(20)-C(19)-H(19A) 109.4 C(18)-C(19)-H(19B) 109.4 C(20)-C(19)-H(19B) 109.4 H(19A)-C(19)-H(19B) 108.0 C(21)-C(20)-C(19) 111.89(13) C(21)-C(20)-H(20A) 109.2 C(19)-C(20)-H(20A) 109.2 C(21)-C(20)-H(20B) 109.2 C(19)-C(20)-H(20B) 109.2 H(20A)-C(20)-H(20B) 107.9 N(3)-C(21)-C(16) 111.20(13) N(3)-C(21)-C(20) 110.13(13) C(16)-C(21)-C(20) 109.60(13) N(3)-C(21)-H(21A) 108.6 C(16)-C(21)-H(21A) 108.6 C(20)-C(21)-H(21A) 108.6 N(3)-C(22)-C(23) 111.37(13) N(3)-C(22)-H(22A) 109.4 C(23)-C(22)-H(22A) 109.4 N(3)-C(22)-H(22B) 109.4 C(23)-C(22)-H(22B) 109.4 H(22A)-C(22)-H(22B) 108.0 O(5)-C(23)-C(22) 108.15(14) O(5)-C(23)-C(24) 110.77(14) C(22)-C(23)-C(24) 111.62(14) O(5)-C(23)-H(23A) 108.7 C(22)-C(23)-H(23A) 108.7 C(24)-C(23)-H(23A) 108.7 N(4)-C(24)-C(23) 111.62(13) N(4)-C(24)-H(24A) 109.3 C(23)-C(24)-H(24A) 109.3 N(4)-C(24)-H(24B) 109.3 C(23)-C(24)-H(24B) 109.3 H(24A)-C(24)-H(24B) 108.0 N(4)-C(25)-C(30) 108.75(12) N(4)-C(25)-C(26) 111.19(13) C(30)-C(25)-C(26) 110.26(14) N(4)-C(25)-H(25A) 108.9 17 Appendix E C(30)-C(25)-H(25A) 108.9 C(26)-C(25)-H(25A) 108.9 C(27)-C(26)-C(25) 112.36(14) C(27)-C(26)-H(26A) 109.1 C(25)-C(26)-H(26A) 109.1 C(27)-C(26)-H(26B) 109.1 C(25)-C(26)-H(26B) 109.1 H(26A)-C(26)-H(26B) 107.9 C(28)-C(27)-C(26) 111.94(15) C(28)-C(27)-H(27A) 109.2 C(26)-C(27)-H(27A) 109.2 C(28)-C(27)-H(27B) 109.2 C(26)-C(27)-H(27B) 109.2 H(27A)-C(27)-H(27B) 107.9 C(27)-C(28)-C(29) 111.02(17) C(27)-C(28)-H(28A) 109.4 C(29)-C(28)-H(28A) 109.4 C(27)-C(28)-H(28B) 109.4 C(29)-C(28)-H(28B) 109.4 H(28A)-C(28)-H(28B) 108.0 C(30)-C(29)-C(28) 109.84(15) C(30)-C(29)-H(29A) 109.7 C(28)-C(29)-H(29A) 109.7 C(30)-C(29)-H(29B) 109.7 C(28)-C(29)-H(29B) 109.7 H(29A)-C(29)-H(29B) 108.2 O(6)-C(30)-C(29) 113.25(13) O(6)-C(30)-C(25) 111.05(13) C(29)-C(30)-C(25) 111.67(13) O(6)-C(30)-H(30A) 106.8 C(29)-C(30)-H(30A) 106.8 C(25)-C(30)-H(30A) 106.8 C(22)-N(3)-C(21) 112.18(13) C(22)-N(3)-H(3N) 107.9(12) C(21)-N(3)-H(3N) 108.3(12) C(24)-N(4)-C(25) 114.56(12) C(24)-N(4)-H(4N) 110.0(12) C(25)-N(4)-H(4N) 106.3(12) C(16)-O(4)-H(4O) 109.5 C(23)-O(5)-H(5O) 109.5 C(30)-O(6)-H(6O) 109.5 H(7O)-O(7)-H(8O) 81.3(16) Symmetry transformations used to generate equivalent atoms: 18 Appendix E Table E.16: Anisotropic displacement parameters (?2x 103)for 7m_al19_0s. The anisotropic displacement factor exponent takes the form: -2p2[ h2a*2U11 + ... + 2 h k a* b* U12 ] U11 U22 U33 U23 U13 U12 C(1) 24(1) 33(1) 27(1) 10(1) 7(1) -1(1) C(2) 36(1) 30(1) 38(1) 9(1) 6(1) 2(1) C(3) 37(1) 43(1) 38(1) 13(1) 12(1) 17(1) C(4) 24(1) 46(1) 46(1) 17(1) 10(1) 9(1) C(5) 23(1) 36(1) 46(1) 12(1) 9(1) 0(1) C(6) 22(1) 31(1) 27(1) 10(1) 6(1) 2(1) C(7) 22(1) 34(1) 34(1) 6(1) 4(1) 1(1) C(8) 21(1) 33(1) 28(1) 8(1) 7(1) 1(1) C(9) 24(1) 36(1) 40(1) 5(1) 6(1) 3(1) C(10) 29(1) 31(1) 35(1) 12(1) 6(1) 3(1) C(11) 32(1) 35(1) 54(1) 13(1) 18(1) 2(1) C(12) 38(1) 40(1) 77(2) 11(1) 14(1) -7(1) C(13) 45(1) 35(1) 69(1) 3(1) 7(1) -2(1) C(14) 37(1) 38(1) 40(1) 3(1) 8(1) 6(1) C(15) 31(1) 39(1) 37(1) 11(1) 10(1) 3(1) N(1) 19(1) 28(1) 32(1) 7(1) 5(1) 0(1) N(2) 25(1) 31(1) 34(1) 7(1) 11(1) 1(1) O(1) 24(1) 40(1) 35(1) 14(1) 5(1) -4(1) O(2) 23(1) 42(1) 31(1) 13(1) 8(1) 2(1) O(3) 33(1) 54(1) 33(1) 11(1) 9(1) -6(1) C(16) 25(1) 40(1) 34(1) 19(1) 5(1) 0(1) C(17) 33(1) 33(1) 50(1) 15(1) 12(1) 6(1) C(18) 30(1) 44(1) 38(1) 7(1) 13(1) 6(1) C(19) 23(1) 45(1) 32(1) 13(1) 11(1) 4(1) C(20) 26(1) 34(1) 30(1) 13(1) 10(1) 4(1) C(21) 19(1) 37(1) 26(1) 11(1) 6(1) 2(1) C(22) 26(1) 47(1) 37(1) 3(1) 11(1) 0(1) C(23) 23(1) 44(1) 32(1) 8(1) 10(1) 3(1) C(24) 25(1) 47(1) 43(1) 1(1) 15(1) 0(1) C(25) 22(1) 35(1) 24(1) 8(1) 6(1) -4(1) C(26) 33(1) 47(1) 33(1) 12(1) 12(1) -12(1) C(27) 46(1) 49(1) 40(1) 12(1) 10(1) -21(1) C(28) 70(1) 32(1) 59(1) 10(1) 22(1) -12(1) C(29) 48(1) 34(1) 49(1) 4(1) 21(1) -3(1) C(30) 29(1) 33(1) 28(1) 11(1) 10(1) -2(1) N(3) 28(1) 39(1) 26(1) 10(1) 11(1) 0(1) N(4) 23(1) 35(1) 28(1) 7(1) 13(1) -2(1) O(4) 40(1) 65(1) 48(1) 39(1) 12(1) 4(1) O(5) 40(1) 57(1) 40(1) 19(1) 21(1) 11(1) O(6) 28(1) 38(1) 29(1) 8(1) 12(1) -4(1) O(7) 49(1) 90(1) 75(1) 49(1) -1(1) -18(1) 19 Appendix E Table E.17: Torsion angles [?] for 7m_al19_0s. O(1)-C(1)-C(2)-C(3) 177.27(13) C(6)-C(1)-C(2)-C(3) 55.95(18) C(1)-C(2)-C(3)-C(4) -56.38(19) C(2)-C(3)-C(4)-C(5) 56.39(19) C(3)-C(4)-C(5)-C(6) -56.25(19) O(1)-C(1)-C(6)-N(1) 59.69(16) C(2)-C(1)-C(6)-N(1) -178.30(13) O(1)-C(1)-C(6)-C(5) -177.24(12) C(2)-C(1)-C(6)-C(5) -55.23(17) C(4)-C(5)-C(6)-N(1) 176.37(13) C(4)-C(5)-C(6)-C(1) 55.36(18) N(1)-C(7)-C(8)-O(2) -63.77(17) N(1)-C(7)-C(8)-C(9) 175.45(13) O(2)-C(8)-C(9)-N(2) 51.38(19) C(7)-C(8)-C(9)-N(2) 170.67(14) N(2)-C(10)-C(11)-C(12) 177.08(14) C(15)-C(10)-C(11)-C(12) -59.75(18) C(10)-C(11)-C(12)-C(13) 57.3(2) C(11)-C(12)-C(13)-C(14) -53.4(2) C(12)-C(13)-C(14)-C(15) 52.0(2) N(2)-C(10)-C(15)-O(3) -51.94(18) C(11)-C(10)-C(15)-O(3) -176.07(14) N(2)-C(10)-C(15)-C(14) -177.88(14) C(11)-C(10)-C(15)-C(14) 57.98(19) C(13)-C(14)-C(15)-O(3) -179.34(15) C(13)-C(14)-C(15)-C(10) -54.1(2) C(8)-C(7)-N(1)-C(6) 164.80(13) C(1)-C(6)-N(1)-C(7) -172.91(13) C(5)-C(6)-N(1)-C(7) 64.54(17) C(8)-C(9)-N(2)-C(10) -165.84(14) C(15)-C(10)-N(2)-C(9) 158.02(14) C(11)-C(10)-N(2)-C(9) -79.04(17) O(4)-C(16)-C(17)-C(18) -179.54(14) C(21)-C(16)-C(17)-C(18) 58.37(18) C(16)-C(17)-C(18)-C(19) -56.08(19) C(17)-C(18)-C(19)-C(20) 54.06(18) C(18)-C(19)-C(20)-C(21) -55.23(18) O(4)-C(16)-C(21)-N(3) 57.42(16) C(17)-C(16)-C(21)-N(3) 179.81(13) O(4)-C(16)-C(21)-C(20) 179.43(12) C(17)-C(16)-C(21)-C(20) -58.19(16) C(19)-C(20)-C(21)-N(3) 179.68(13) C(19)-C(20)-C(21)-C(16) 57.04(17) N(3)-C(22)-C(23)-O(5) -61.64(18) N(3)-C(22)-C(23)-C(24) 176.27(14) 20 Appendix E O(5)-C(23)-C(24)-N(4) 77.77(18) C(22)-C(23)-C(24)-N(4) -161.66(14) N(4)-C(25)-C(26)-C(27) -173.86(14) C(30)-C(25)-C(26)-C(27) -53.16(18) C(25)-C(26)-C(27)-C(28) 53.2(2) C(26)-C(27)-C(28)-C(29) -54.9(2) C(27)-C(28)-C(29)-C(30) 57.1(2) C(28)-C(29)-C(30)-O(6) 175.32(15) C(28)-C(29)-C(30)-C(25) -58.4(2) N(4)-C(25)-C(30)-O(6) -54.17(16) C(26)-C(25)-C(30)-O(6) -176.32(12) N(4)-C(25)-C(30)-C(29) 178.38(13) C(26)-C(25)-C(30)-C(29) 56.23(17) C(23)-C(22)-N(3)-C(21) -178.77(13) C(16)-C(21)-N(3)-C(22) -157.87(13) C(20)-C(21)-N(3)-C(22) 80.44(17) C(23)-C(24)-N(4)-C(25) -170.91(14) C(30)-C(25)-N(4)-C(24) 175.43(13) C(26)-C(25)-N(4)-C(24) -62.98(18) Symmetry transformations used to generate equivalent atoms: Table E.18: Hydrogen bonds for 7m_al19_0s [? and ?]. D-H...A d(D-H) d(H...A) d(D...A) <(DHA) N(1)-H(1N)...O(1) 0.848(17) 2.400(17) 2.8057(17) 110.1(13) N(2)-H(2N)...O(3) 0.836(18) 2.335(17) 2.7926(18) 114.9(14) N(2)-H(2N)...O(2) 0.836(18) 2.450(17) 2.8543(18) 110.7(14) N(3)-H(3N)...O(4) 0.816(17) 2.424(17) 2.842(2) 112.8(14) N(4)-H(4N)...O(6) 0.794(17) 2.398(16) 2.7912(16) 111.7(14) Symmetry transformations used to generate equivalent atoms: 21 Appendix E BHEEN Data Figure E.4: XRD structure of the nitrate salt of BHEEN and the labelling scheme used Table E.19: Crystal data and structure refinement for 8m_alv11_0s. Identification code 8m_alv11_0s Empirical formula C6 H18 N4 O8 Formula weight 274.24 Temperature 173(2) K Wavelength 0.71073 ? Crystal system Orthorhombic Space group Pbca Unit cell dimensions a = 7.6230(3) ? ? = 90? b = 10.0645(5) ? ? = 90? c = 15.6002(9) ? ? = 90? Volume 1196.87(10) ?3 Z 4 Density (calculated) 1.522 Mg/m3 Absorption coefficient 0.140 mm-1 F(000) 584 Crystal size 0.43 x 0.36 x 0.09 mm3 Theta range for data collection 2.61 to 27.98?. Index ranges -8?h?10, -12?k?13, -20?l?10 Reflections collected 6852 Independent reflections 1437 [R(int) = 0.0373] Completeness to theta = 27.98? 99.8 % Absorption correction None Max. and min. transmission 0.9875 and 0.9423 Refinement method Full-matrix least-squares on F2 22 Appendix E Data / restraints / parameters 1437 / 0 / 86 Goodness-of-fit on F2 1.069 Final R indices [I>2?(I)] R1 = 0.0327, wR2 = 0.0842 R indices (all data) R1 = 0.0425, wR2 = 0.0877 Largest diff. peak and hole 0.323 and -0.210 e.?-3 Table E.20: Atomic coordinates ( x 104) and equivalent isotropic displacement parameters (?2 x 103) for 8m_alv11_0s. U(eq) is defined as one third of the trace of the orthogonalized Uij tensor. x y z U(eq) C(1) 172(2) 2700(1) 7147(1) 27(1) C(2) 394(2) 1312(1) 6798(1) 24(1) C(3) 163(2) -42(1) 5479(1) 22(1) N(1) 62(1) 1307(1) 5857(1) 19(1) N(2) 616(1) 3791(1) 4251(1) 24(1) O(1) 1369(1) 3568(1) 6738(1) 31(1) O(2) -931(1) 3803(1) 4466(1) 40(1) O(3) 1655(1) 2949(1) 4571(1) 29(1) O(4) 1210(1) 4589(1) 3713(1) 34(1) Table E.21: Bond lengths [?] and angles [?] for 8m_alv11_0s. C(1)-O(1) 1.4152(15) C(1)-C(2) 1.5083(15) C(1)-H(1A) 0.9900 C(1)-H(1B) 0.9900 C(2)-N(1) 1.4888(15) C(2)-H(2A) 0.9900 C(2)-H(2B) 0.9900 C(3)-N(1) 1.4823(13) C(3)-C(3)#1 1.517(2) C(3)-H(3A) 0.9900 C(3)-H(3B) 0.9900 N(1)-H(1N) 0.9200 N(1)-H(2N) 0.9200 N(2)-O(2) 1.2260(13) N(2)-O(4) 1.2459(13) N(2)-O(3) 1.2630(12) O(1)-H(1O) 0.788(17) 23 Appendix E O(1)-C(1)-C(2) 109.67(10) O(1)-C(1)-H(1A) 109.7 C(2)-C(1)-H(1A) 109.7 O(1)-C(1)-H(1B) 109.7 C(2)-C(1)-H(1B) 109.7 H(1A)-C(1)-H(1B) 108.2 N(1)-C(2)-C(1) 109.87(9) N(1)-C(2)-H(2A) 109.7 C(1)-C(2)-H(2A) 109.7 N(1)-C(2)-H(2B) 109.7 C(1)-C(2)-H(2B) 109.7 H(2A)-C(2)-H(2B) 108.2 N(1)-C(3)-C(3)#1 109.45(11) N(1)-C(3)-H(3A) 109.8 C(3)#1-C(3)-H(3A) 109.8 N(1)-C(3)-H(3B) 109.8 C(3)#1-C(3)-H(3B) 109.8 H(3A)-C(3)-H(3B) 108.2 C(3)-N(1)-C(2) 112.74(8) C(3)-N(1)-H(1N) 109.0 C(2)-N(1)-H(1N) 109.0 C(3)-N(1)-H(2N) 109.0 C(2)-N(1)-H(2N) 109.0 H(1N)-N(1)-H(2N) 107.8 O(2)-N(2)-O(4) 121.82(10) O(2)-N(2)-O(3) 120.05(10) O(4)-N(2)-O(3) 118.13(9) C(1)-O(1)-H(1O) 104.4(12) Symmetry transformations used to generate equivalent atoms: #1 -x,-y,-z+1 24 Appendix E Table E.22: Anisotropic displacement parameters (?2 x 103)for 8m_alv11_0s. The anisotropic displacement factor exponent takes the form: -2p2[ h2a*2U11 + ... + 2 h k a* b* U12 ] U11 U22 U33 U23 U13 C(1) 34(1) 25(1) 23(1) -1(1) 1(1) C(2) 29(1) 22(1) 21(1) 1(1) -3(1) C(3) 25(1) 17(1) 22(1) 0(1) -1(1) N(1) 19(1) 18(1) 21(1) 2(1) -1(1) N(2) 24(1) 22(1) 24(1) -3(1) -2(1) O(1) 31(1) 23(1) 41(1) 2(1) -4(1) O(2) 19(1) 46(1) 56(1) 0(1) 3(1) O(3) 25(1) 26(1) 36(1) 10(1) 1(1) O(4) 39(1) 32(1) 31(1) 12(1) 2(1) Table E.23: Torsion angles [?] for 8m_alv11_0s. C(3)#1-C(3)-N(1)-C(2) -179.16(11) C(1)-C(2)-N(1)-C(3) -176.90(9) Symmetry transformations used to generate equivalent atoms: #1 -x,-y,-z+1 Table E.24: Hydrogen bonds for 8m_alv11_0s [? and ?]. D-H...A d(D-H) d(H...A) d(D...A) <(DHA) N(1)-H(1N)...O(3)#2 0.92 1.88 2.7843(12) 168.8 O(1)-H(1O)...O(4)#3 0.788(17) 2.022(16) 2.7924(13) 165.5(16) Symmetry transformations used to generate equivalent atoms: #1 -x,-y,-z+1 #2 x-1/2,-y+1/2,-z+1 #3 -x,-y+1,-z+1 25 Appendix E Cy2-en/Pb complex Figure E.5: XRD structure of the lead(II) complex of Cy2-en and the labelling scheme used Table E.25: Crystal data and structure refinement for 7m_al10_0a. Identification code 7m_al10_0a Empirical formula C14 H26 N4 O8 Pb Formula weight 585.58 Temperature 273(2) K Wavelength 0.71073 ? Crystal system Monoclinic Space group P2(1) Unit cell dimensions a = 9.0573(2) ? ? = 90?. b = 9.7265(2) ? ? = 107.4940(10)?. c = 11.4533(2) ? ? = 90?. Volume 962.32(3) ?3 Z 2 Density (calculated) 2.021 Mg/m3 Absorption coefficient 8.815 mm-1 F(000) 568 Crystal size 0.31 x 0.14 x 0.13 mm3 Theta range for data collection 1.86 to 28.00?. Index ranges -11<=h<=11, -12<=k<=12, -14<=l<=15 Reflections collected 16110 Independent reflections 4640 [R(int) = 0.0608] 26 Appendix E Completeness to theta = 28.00? 100.0 % Absorption correction Integration Max. and min. transmission 0.3936 and 0.1708 Refinement method Full-matrix least-squares on F2 Data / restraints / parameters 4640 / 1 / 244 Goodness-of-fit on F2 1.013 Final R indices [I>2sigma(I)] R1 = 0.0196, wR2 = 0.0441 R indices (all data) R1 = 0.0212, wR2 = 0.0444 Absolute structure parameter -0.012(5) Largest diff. peak and hole 0.793 and -0.731 e.?-3 Table E.26: Atomic coordinates ( x 104) and equivalent isotropic displacement parameters (?2x 103) for 7m_al10_0a. U(eq) is defined as one third of the trace of the orthogonalized Uij tensor. x y z U(eq) C(1) 3432(3) 2217(7) 2714(2) 24(1) C(2) 2981(5) 1728(4) 3815(3) 28(1) C(3) 3886(4) 2513(4) 4956(3) 33(1) C(4) 3566(5) 4051(4) 4767(3) 34(1) C(5) 3987(5) 4543(4) 3632(3) 31(1) C(6) 3121(4) 3727(4) 2494(3) 24(1) C(7) 2509(5) 5252(4) 684(3) 30(1) C(8) 1182(4) 4591(4) -288(3) 27(1) C(9) 572(5) 3142(4) -2133(3) 22(1) C(10) 39(5) 4099(4) -3257(4) 34(1) C(11) -1243(5) 3404(4) -4286(4) 35(1) C(12) -706(5) 2038(6) -4637(3) 37(1) C(13) -164(6) 1090(5) -3511(4) 37(1) C(14) 1112(5) 1799(4) -2497(3) 29(1) N(1) 3552(4) 4187(3) 1413(2) 26(1) N(2) 1796(4) 3818(4) -1129(3) 23(1) N(3) 2368(5) 7621(4) -2032(3) 36(1) N(4) 5723(4) 3466(3) -1619(3) 30(1) O(1) 2535(3) 1517(3) 1606(2) 27(1) O(2) 1578(5) 941(3) -1414(3) 44(1) O(3) 2975(4) 8751(4) -2151(4) 51(1) O(4) 1032(4) 7600(4) -2003(4) 74(1) O(5) 3125(5) 6558(4) -1937(3) 45(1) O(6) 5540(4) 4147(3) -728(3) 44(1) O(7) 4901(4) 2454(4) -1996(2) 35(1) O(8) 6744(4) 3821(3) -2077(3) 43(1) Pb(1) 3832(1) 2229(1) 69(1) 27(1) 27 Appendix E Table E.27: Bond lengths [?] and angles [?] for 7m_al10_0a. C(1)-O(1) 1.454(4) C(1)-C(6) 1.502(8) C(1)-C(2) 1.514(5) C(1)-H(1A) 0.9800 C(2)-C(3) 1.523(5) C(2)-H(2A) 0.9700 C(2)-H(2B) 0.9700 C(3)-C(4) 1.527(6) C(3)-H(3A) 0.9700 C(3)-H(3B) 0.9700 C(4)-C(5) 1.536(5) C(4)-H(4A) 0.9700 C(4)-H(4B) 0.9700 C(5)-C(6) 1.526(5) C(5)-H(5A) 0.9700 C(5)-H(5B) 0.9700 C(6)-N(1) 1.476(4) C(6)-H(6A) 0.9800 C(7)-N(1) 1.479(5) C(7)-C(8) 1.514(5) C(7)-H(7A) 0.9700 C(7)-H(7B) 0.9700 C(8)-N(2) 1.458(5) C(8)-H(8A) 0.9700 C(8)-H(8B) 0.9700 C(9)-N(2) 1.489(5) C(9)-C(14) 1.497(5) C(9)-C(10) 1.544(5) C(9)-H(9A) 0.9800 C(10)-C(11) 1.540(5) C(10)-H(10A) 0.9700 C(10)-H(10B) 0.9700 C(11)-C(12) 1.510(7) C(11)-H(11A) 0.9700 C(11)-H(11B) 0.9700 C(12)-C(13) 1.540(6) C(12)-H(12A) 0.9700 C(12)-H(12B) 0.9700 C(13)-C(14) 1.534(5) C(13)-H(13A) 0.9700 C(13)-H(13B) 0.9700 C(14)-O(2) 1.448(5) C(14)-H(14) 0.9800 N(1)-Pb(1) 2.509(3) N(1)-H(1N) 0.9100 28 Appendix E N(2)-Pb(1) 2.480(4) N(2)-H(2N) 0.9100 N(3)-O(4) 1.221(5) N(3)-O(5) 1.227(5) N(3)-O(3) 1.254(5) N(4)-O(7) 1.231(5) N(4)-O(8) 1.241(5) N(4)-O(6) 1.269(4) O(1)-Pb(1) 2.491(3) O(2)-Pb(1) 2.557(4) O(6)-Pb(1) 2.748(3) O(1)-C(1)-C(6) 106.5(3) O(1)-C(1)-C(2) 111.1(4) C(6)-C(1)-C(2) 111.3(3) O(1)-C(1)-H(1A) 109.3 C(6)-C(1)-H(1A) 109.3 C(2)-C(1)-H(1A) 109.3 C(1)-C(2)-C(3) 110.3(3) C(1)-C(2)-H(2A) 109.6 C(3)-C(2)-H(2A) 109.6 C(1)-C(2)-H(2B) 109.6 C(3)-C(2)-H(2B) 109.6 H(2A)-C(2)-H(2B) 108.1 C(2)-C(3)-C(4) 109.8(3) C(2)-C(3)-H(3A) 109.7 C(4)-C(3)-H(3A) 109.7 C(2)-C(3)-H(3B) 109.7 C(4)-C(3)-H(3B) 109.7 H(3A)-C(3)-H(3B) 108.2 C(3)-C(4)-C(5) 109.9(3) C(3)-C(4)-H(4A) 109.7 C(5)-C(4)-H(4A) 109.7 C(3)-C(4)-H(4B) 109.7 C(5)-C(4)-H(4B) 109.7 H(4A)-C(4)-H(4B) 108.2 C(6)-C(5)-C(4) 111.5(3) C(6)-C(5)-H(5A) 109.3 C(4)-C(5)-H(5A) 109.3 C(6)-C(5)-H(5B) 109.3 C(4)-C(5)-H(5B) 109.3 H(5A)-C(5)-H(5B) 108.0 N(1)-C(6)-C(1) 110.7(3) N(1)-C(6)-C(5) 111.2(3) C(1)-C(6)-C(5) 110.1(3) N(1)-C(6)-H(6A) 108.2 29 Appendix E C(1)-C(6)-H(6A) 108.2 C(5)-C(6)-H(6A) 108.2 N(1)-C(7)-C(8) 110.4(3) N(1)-C(7)-H(7A) 109.6 C(8)-C(7)-H(7A) 109.6 N(1)-C(7)-H(7B) 109.6 C(8)-C(7)-H(7B) 109.6 H(7A)-C(7)-H(7B) 108.1 N(2)-C(8)-C(7) 109.1(3) N(2)-C(8)-H(8A) 109.9 C(7)-C(8)-H(8A) 109.9 N(2)-C(8)-H(8B) 109.9 C(7)-C(8)-H(8B) 109.9 H(8A)-C(8)-H(8B) 108.3 N(2)-C(9)-C(14) 111.8(3) N(2)-C(9)-C(10) 110.5(3) C(14)-C(9)-C(10) 109.9(3) N(2)-C(9)-H(9A) 108.2 C(14)-C(9)-H(9A) 108.2 C(10)-C(9)-H(9A) 108.2 C(11)-C(10)-C(9) 110.4(3) C(11)-C(10)-H(10A) 109.6 C(9)-C(10)-H(10A) 109.6 C(11)-C(10)-H(10B) 109.6 C(9)-C(10)-H(10B) 109.6 H(10A)-C(10)-H(10B) 108.1 C(12)-C(11)-C(10) 111.1(4) C(12)-C(11)-H(11A) 109.4 C(10)-C(11)-H(11A) 109.4 C(12)-C(11)-H(11B) 109.4 C(10)-C(11)-H(11B) 109.4 H(11A)-C(11)-H(11B) 108.0 C(11)-C(12)-C(13) 110.6(3) C(11)-C(12)-H(12A) 109.5 C(13)-C(12)-H(12A) 109.5 C(11)-C(12)-H(12B) 109.5 C(13)-C(12)-H(12B) 109.5 H(12A)-C(12)-H(12B) 108.1 C(14)-C(13)-C(12) 110.0(4) C(14)-C(13)-H(13A) 109.7 C(12)-C(13)-H(13A) 109.7 C(14)-C(13)-H(13B) 109.7 C(12)-C(13)-H(13B) 109.7 H(13A)-C(13)-H(13B) 108.2 O(2)-C(14)-C(9) 107.4(3) O(2)-C(14)-C(13) 110.4(3) 30 Appendix E C(9)-C(14)-C(13) 111.6(3) O(2)-C(14)-H(14) 109.1 C(9)-C(14)-H(14) 109.1 C(13)-C(14)-H(14) 109.1 C(6)-N(1)-C(7) 113.6(3) C(6)-N(1)-Pb(1) 112.7(2) C(7)-N(1)-Pb(1) 110.5(2) C(6)-N(1)-H(1N) 106.5 C(7)-N(1)-H(1N) 106.5 Pb(1)-N(1)-H(1N) 106.5 C(8)-N(2)-C(9) 113.2(3) C(8)-N(2)-Pb(1) 108.9(2) C(9)-N(2)-Pb(1) 114.1(2) C(8)-N(2)-H(2N) 106.7 C(9)-N(2)-H(2N) 106.7 Pb(1)-N(2)-H(2N) 106.7 O(4)-N(3)-O(5) 121.0(4) O(4)-N(3)-O(3) 119.2(4) O(5)-N(3)-O(3) 119.8(4) O(7)-N(4)-O(8) 121.6(4) O(7)-N(4)-O(6) 119.1(4) O(8)-N(4)-O(6) 119.3(4) C(1)-O(1)-Pb(1) 103.2(2) C(14)-O(2)-Pb(1) 104.8(2) N(4)-O(6)-Pb(1) 97.8(2) N(2)-Pb(1)-O(1) 97.73(11) N(2)-Pb(1)-N(1) 70.80(10) O(1)-Pb(1)-N(1) 67.76(9) N(2)-Pb(1)-O(2) 68.01(11) O(1)-Pb(1)-O(2) 83.18(10) N(1)-Pb(1)-O(2) 124.89(11) N(2)-Pb(1)-O(6) 78.02(11) O(1)-Pb(1)-O(6) 148.84(8) N(1)-Pb(1)-O(6) 81.91(9) O(2)-Pb(1)-O(6) 121.91(10) 31 Appendix E Table E.28: Anisotropic displacement parameters (?2x 103)for 7m_al10_0a. The anisotropic displacement factor exponent takes the form: -2p2[ h2a*2U11 + ... + 2 h k a* b* U12 ] U11 U22 U33 U23 U13 U12 C(1) 22(1) 28(1) 21(1) -1(3) 6(1) -2(2) C(2) 29(2) 29(2) 29(2) 3(1) 12(2) 1(1) C(3) 35(2) 44(4) 21(2) 6(2) 6(2) 4(2) C(4) 41(2) 37(2) 20(2) -3(2) 6(2) 0(2) C(5) 39(2) 28(2) 22(2) -3(1) 4(2) -5(2) C(6) 25(2) 25(2) 21(2) -1(1) 8(1) -4(1) C(7) 41(2) 25(2) 22(2) -2(1) 7(2) -8(2) C(8) 29(2) 26(2) 23(2) -1(1) 5(2) 4(1) C(9) 20(2) 24(2) 22(2) 1(1) 4(2) -1(1) C(10) 37(2) 28(2) 30(2) 3(2) 0(2) 1(2) C(11) 36(2) 41(2) 23(2) -3(2) 0(2) -1(2) C(12) 36(2) 54(4) 21(1) -8(2) 6(1) -4(2) C(13) 43(3) 34(2) 33(2) -12(2) 10(2) -7(2) C(14) 34(2) 26(2) 23(2) 0(1) 3(2) 1(1) N(1) 23(2) 34(2) 21(1) 1(1) 6(1) -8(1) N(2) 23(2) 24(2) 20(2) -2(1) 5(1) -2(1) N(3) 28(2) 48(3) 29(2) 4(1) 6(2) -6(2) N(4) 31(2) 33(2) 28(2) 12(1) 11(2) 6(1) O(1) 30(1) 28(1) 24(1) -7(1) 10(1) -6(1) O(2) 67(3) 23(2) 30(2) 1(1) -1(2) 2(2) O(3) 44(2) 40(2) 73(2) -12(2) 24(2) -13(2) O(4) 34(2) 75(4) 116(3) 24(2) 29(2) 5(2) O(5) 42(2) 36(2) 55(2) 12(2) 16(2) 10(2) O(6) 52(2) 38(2) 51(2) -16(1) 33(2) -7(1) O(7) 44(2) 35(2) 26(1) -5(1) 10(1) -13(2) O(8) 50(2) 41(2) 51(2) 3(1) 35(2) -1(1) Pb(1) 26(1) 35(1) 21(1) 5(1) 10(1) 9(1) Table E.29: Torsion angles [?] for 7m_al10_0a. O(1)-C(1)-C(2)-C(3) -177.8(4) C(6)-C(1)-C(2)-C(3) -59.2(4) C(1)-C(2)-C(3)-C(4) 58.9(4) C(2)-C(3)-C(4)-C(5) -57.2(4) C(3)-C(4)-C(5)-C(6) 56.3(4) O(1)-C(1)-C(6)-N(1) -58.3(3) C(2)-C(1)-C(6)-N(1) -179.5(3) O(1)-C(1)-C(6)-C(5) 178.4(3) C(2)-C(1)-C(6)-C(5) 57.2(4) 32 Appendix E C(4)-C(5)-C(6)-N(1) -179.0(3) C(4)-C(5)-C(6)-C(1) -55.9(4) N(1)-C(7)-C(8)-N(2) -62.5(4) N(2)-C(9)-C(10)-C(11) -179.2(4) C(14)-C(9)-C(10)-C(11) 57.0(5) C(9)-C(10)-C(11)-C(12) -56.7(5) C(10)-C(11)-C(12)-C(13) 56.5(5) C(11)-C(12)-C(13)-C(14) -56.3(5) N(2)-C(9)-C(14)-O(2) 57.6(4) C(10)-C(9)-C(14)-O(2) -179.3(3) N(2)-C(9)-C(14)-C(13) 178.7(3) C(10)-C(9)-C(14)-C(13) -58.2(5) C(12)-C(13)-C(14)-O(2) 177.3(4) C(12)-C(13)-C(14)-C(9) 57.9(5) C(1)-C(6)-N(1)-C(7) 143.9(3) C(5)-C(6)-N(1)-C(7) -93.3(4) C(1)-C(6)-N(1)-Pb(1) 17.3(3) C(5)-C(6)-N(1)-Pb(1) 140.0(3) C(8)-C(7)-N(1)-C(6) -89.8(4) C(8)-C(7)-N(1)-Pb(1) 38.1(4) C(7)-C(8)-N(2)-C(9) -179.3(3) C(7)-C(8)-N(2)-Pb(1) 52.6(3) C(14)-C(9)-N(2)-C(8) -146.2(3) C(10)-C(9)-N(2)-C(8) 91.0(4) C(14)-C(9)-N(2)-Pb(1) -20.9(4) C(10)-C(9)-N(2)-Pb(1) -143.6(3) C(6)-C(1)-O(1)-Pb(1) 67.9(2) C(2)-C(1)-O(1)-Pb(1) -170.7(3) C(9)-C(14)-O(2)-Pb(1) -62.5(3) C(13)-C(14)-O(2)-Pb(1) 175.7(3) O(7)-N(4)-O(6)-Pb(1) 15.4(4) O(8)-N(4)-O(6)-Pb(1) -163.3(3) C(8)-N(2)-Pb(1)-O(1) 39.7(3) C(9)-N(2)-Pb(1)-O(1) -88.0(3) C(8)-N(2)-Pb(1)-N(1) -23.5(2) C(9)-N(2)-Pb(1)-N(1) -151.1(3) C(8)-N(2)-Pb(1)-O(2) 119.1(3) C(9)-N(2)-Pb(1)-O(2) -8.6(2) C(8)-N(2)-Pb(1)-O(6) -109.0(3) C(9)-N(2)-Pb(1)-O(6) 123.4(3) C(1)-O(1)-Pb(1)-N(2) -107.3(3) C(1)-O(1)-Pb(1)-N(1) -41.8(3) C(1)-O(1)-Pb(1)-O(2) -174.0(3) C(1)-O(1)-Pb(1)-O(6) -27.7(3) C(6)-N(1)-Pb(1)-N(2) 120.3(3) C(7)-N(1)-Pb(1)-N(2) -8.0(2) 33 Appendix E C(6)-N(1)-Pb(1)-O(1) 13.1(2) C(7)-N(1)-Pb(1)-O(1) -115.2(3) C(6)-N(1)-Pb(1)-O(2) 76.9(2) C(7)-N(1)-Pb(1)-O(2) -51.4(3) C(6)-N(1)-Pb(1)-O(6) -159.6(2) C(7)-N(1)-Pb(1)-O(6) 72.1(2) C(14)-O(2)-Pb(1)-N(2) 37.2(2) C(14)-O(2)-Pb(1)-O(1) 138.4(3) C(14)-O(2)-Pb(1)-N(1) 81.6(3) C(14)-O(2)-Pb(1)-O(6) -21.8(3) N(4)-O(6)-Pb(1)-N(2) -99.7(2) N(4)-O(6)-Pb(1)-O(1) 175.2(2) N(4)-O(6)-Pb(1)-N(1) -171.7(2) N(4)-O(6)-Pb(1)-O(2) -45.4(3) Symmetry transformations used to generate equivalent atoms: Table E.30: Hydrogen bonds for 7m_al10_0a [? and ?]. D-H...A d(D-H) d(H...A) d(D...A) <(DHA) N(1)-H(1N)...O(3)#1 0.91 2.33 3.031(5) 133.8 N(2)-H(2N)...O(5) 0.91 2.31 3.174(5) 157.9 Symmetry transformations used to generate equivalent atoms: #1 -x+1,y-1/2,-z 34 Appendix E Cy2-en/Cd Data Figure E.6: The XRD structure of the cadmium(II) complex of Cy2-en and the labelling scheme used Table E.31: Crystal data and structure refinement for 7m_al7_a. Identification code 7m_al7_a Empirical formula C15 H28 Cd Cl2 N2 O3 Formula weight 467.69 Temperature 223(2) K Wavelength 0.71073 ? Crystal system Triclinic Space group P-1 Unit cell dimensions a = 7.6698(7) ? ? = 75.694(4)? b = 11.0270(10) ? ? = 80.960(4)? c = 12.4807(13) ? ? = 81.170(4). Volume 1002.84(17) ?3 Z 2 Density (calculated) 1.549 Mg/m3 Absorption coefficient 1.369 mm-1 F(000) 476 Crystal size 0.44 x 0.26 x 0.06 mm3 Theta range for data collection 1.70 to 23.90?. Index ranges -7?h?8, -12?k?11, -13?l?13 Reflections collected 8065 Independent reflections 2523 [R(int) = 0.0385] Completeness to theta = 23.90? 80.9 % 35 Appendix E Absorption correction Integration Max. and min. transmission 0.9224 and 0.5842 Refinement method Full-matrix least-squares on F2 Data / restraints / parameters 2523 / 0 / 214 Goodness-of-fit on F2 1.068 Final R indices [I>2?(I)] R1 = 0.0280, wR2 = 0.0697 R indices (all data) R1 = 0.0304, wR2 = 0.0713 Largest diff. peak and hole 1.029 and -0.682 e.?-3 Table E.32: Atomic coordinates ( x 104) and equivalent isotropic displacement parameters (?2 x 103) for 7m_al7_a. U(eq) is defined as one third of the trace of the orthogonalized Uij tensor. x y z U(eq) C(1) -4381(6) 847(4) 7002(3) 32(1) C(2) -5694(6) 716(4) 8070(4) 40(1) C(3) -5241(7) 1463(5) 8841(4) 51(1) C(4) -5175(8) 2835(5) 8249(4) 59(2) C(5) -3855(7) 2957(4) 7178(4) 50(1) C(6) -4349(6) 2223(4) 6415(3) 33(1) C(7) -3476(6) 3549(4) 4569(3) 36(1) C(8) -2273(6) 3630(4) 3480(3) 35(1) C(9) 902(5) 3319(4) 2703(3) 29(1) C(10) 888(6) 4437(4) 1697(3) 41(1) C(11) 2319(7) 4189(5) 740(4) 47(1) C(12) 4138(6) 3824(4) 1132(4) 44(1) C(13) 4115(6) 2698(4) 2134(3) 36(1) C(14) 2745(5) 2994(4) 3075(3) 30(1) C(15) -710(20) 1728(17) -220(30) 410(20) N(1) -3099(4) 2322(3) 5356(3) 29(1) N(2) -411(4) 3524(3) 3664(3) 28(1) O(1) -4790(4) 146(3) 6257(2) 34(1) O(2) 2750(4) 1993(3) 4060(2) 36(1) O(3) 350(20) 1208(12) 813(12) 314(9) Cl(1) 1024(1) -214(1) 6295(1) 36(1) Cl(2) 833(2) 3398(1) 6350(1) 47(1) Cd(1) 29(1) 1971(1) 5281(1) 31(1) 36 Appendix E Table E.33: Bond lengths [?] and angles [?] for 7m_al7_a. C(1)-O(1) 1.441(5) C(1)-C(6) 1.516(6) C(1)-C(2) 1.530(6) C(1)-H(1A) 0.9900 C(2)-C(3) 1.520(7) C(2)-H(2A) 0.9800 C(2)-H(2B) 0.9800 C(3)-C(4) 1.515(7) C(3)-H(3A) 0.9800 C(3)-H(3B) 0.9800 C(4)-C(5) 1.535(7) C(4)-H(4A) 0.9800 C(4)-H(4B) 0.9800 C(5)-C(6) 1.514(6) C(5)-H(5A) 0.9800 C(5)-H(5B) 0.9800 C(6)-N(1) 1.497(5) C(6)-H(6A) 0.9900 C(7)-N(1) 1.481(5) C(7)-C(8) 1.509(6) C(7)-H(7A) 0.9800 C(7)-H(7B) 0.9800 C(8)-N(2) 1.464(5) C(8)-H(8A) 0.9800 C(8)-H(8B) 0.9800 C(9)-N(2) 1.480(5) C(9)-C(14) 1.519(6) C(9)-C(10) 1.527(6) C(9)-H(9A) 0.9900 C(10)-C(11) 1.537(6) C(10)-H(10A) 0.9800 C(10)-H(10B) 0.9800 C(11)-C(12) 1.514(7) C(11)-H(11A) 0.9800 C(11)-H(11B) 0.9800 C(12)-C(13) 1.529(6) C(12)-H(12A) 0.9800 C(12)-H(12B) 0.9800 C(13)-C(14) 1.512(6) C(13)-H(13A) 0.9800 C(13)-H(13B) 0.9800 C(14)-O(2) 1.436(5) C(14)-H(14A) 0.9900 C(15)-O(3) 1.58(3) N(1)-Cd(1) 2.361(3) 37 Appendix E N(1)-H(1N) 0.9200 N(2)-Cd(1) 2.334(3) N(2)-H(2N) 0.9200 O(1)-H(1O) 0.8300 O(2)-Cd(1) 2.383(3) O(2)-H(2O) 0.75(4) Cl(1)-Cd(1) 2.4935(10) Cl(2)-Cd(1) 2.4955(11) O(1)-C(1)-C(6) 110.1(3) O(1)-C(1)-C(2) 112.0(3) C(6)-C(1)-C(2) 110.4(3) O(1)-C(1)-H(1A) 108.1 C(6)-C(1)-H(1A) 108.1 C(2)-C(1)-H(1A) 108.1 C(3)-C(2)-C(1) 111.1(4) C(3)-C(2)-H(2A) 109.4 C(1)-C(2)-H(2A) 109.4 C(3)-C(2)-H(2B) 109.4 C(1)-C(2)-H(2B) 109.4 H(2A)-C(2)-H(2B) 108.0 C(4)-C(3)-C(2) 110.8(4) C(4)-C(3)-H(3A) 109.5 C(2)-C(3)-H(3A) 109.5 C(4)-C(3)-H(3B) 109.5 C(2)-C(3)-H(3B) 109.5 H(3A)-C(3)-H(3B) 108.1 C(3)-C(4)-C(5) 110.8(4) C(3)-C(4)-H(4A) 109.5 C(5)-C(4)-H(4A) 109.5 C(3)-C(4)-H(4B) 109.5 C(5)-C(4)-H(4B) 109.5 H(4A)-C(4)-H(4B) 108.1 C(6)-C(5)-C(4) 110.4(4) C(6)-C(5)-H(5A) 109.6 C(4)-C(5)-H(5A) 109.6 C(6)-C(5)-H(5B) 109.6 C(4)-C(5)-H(5B) 109.6 H(5A)-C(5)-H(5B) 108.1 N(1)-C(6)-C(5) 112.2(3) N(1)-C(6)-C(1) 109.3(3) C(5)-C(6)-C(1) 110.5(4) N(1)-C(6)-H(6A) 108.3 C(5)-C(6)-H(6A) 108.3 C(1)-C(6)-H(6A) 108.3 N(1)-C(7)-C(8) 111.5(3) 38 Appendix E N(1)-C(7)-H(7A) 109.3 C(8)-C(7)-H(7A) 109.3 N(1)-C(7)-H(7B) 109.3 C(8)-C(7)-H(7B) 109.3 H(7A)-C(7)-H(7B) 108.0 N(2)-C(8)-C(7) 110.4(3) N(2)-C(8)-H(8A) 109.6 C(7)-C(8)-H(8A) 109.6 N(2)-C(8)-H(8B) 109.6 C(7)-C(8)-H(8B) 109.6 H(8A)-C(8)-H(8B) 108.1 N(2)-C(9)-C(14) 109.0(3) N(2)-C(9)-C(10) 113.9(3) C(14)-C(9)-C(10) 110.2(3) N(2)-C(9)-H(9A) 107.9 C(14)-C(9)-H(9A) 107.9 C(10)-C(9)-H(9A) 107.9 C(9)-C(10)-C(11) 111.7(4) C(9)-C(10)-H(10A) 109.3 C(11)-C(10)-H(10A) 109.3 C(9)-C(10)-H(10B) 109.3 C(11)-C(10)-H(10B) 109.3 H(10A)-C(10)-H(10B) 108.0 C(12)-C(11)-C(10) 111.2(4) C(12)-C(11)-H(11A) 109.4 C(10)-C(11)-H(11A) 109.4 C(12)-C(11)-H(11B) 109.4 C(10)-C(11)-H(11B) 109.4 H(11A)-C(11)-H(11B) 108.0 C(11)-C(12)-C(13) 110.7(4) C(11)-C(12)-H(12A) 109.5 C(13)-C(12)-H(12A) 109.5 C(11)-C(12)-H(12B) 109.5 C(13)-C(12)-H(12B) 109.5 H(12A)-C(12)-H(12B) 108.1 C(14)-C(13)-C(12) 110.6(4) C(14)-C(13)-H(13A) 109.5 C(12)-C(13)-H(13A) 109.5 C(14)-C(13)-H(13B) 109.5 C(12)-C(13)-H(13B) 109.5 H(13A)-C(13)-H(13B) 108.1 O(2)-C(14)-C(13) 112.6(3) O(2)-C(14)-C(9) 110.7(3) C(13)-C(14)-C(9) 110.7(3) O(2)-C(14)-H(14A) 107.6 C(13)-C(14)-H(14A) 107.6 39 Appendix E C(9)-C(14)-H(14A) 107.6 C(7)-N(1)-C(6) 111.3(3) C(7)-N(1)-Cd(1) 105.2(2) C(6)-N(1)-Cd(1) 124.0(3) C(7)-N(1)-H(1N) 104.9 C(6)-N(1)-H(1N) 104.9 Cd(1)-N(1)-H(1N) 104.9 C(8)-N(2)-C(9) 114.9(3) C(8)-N(2)-Cd(1) 108.3(2) C(9)-N(2)-Cd(1) 112.5(2) C(8)-N(2)-H(2N) 106.9 C(9)-N(2)-H(2N) 106.9 Cd(1)-N(2)-H(2N) 106.9 C(1)-O(1)-H(1O) 109.5 C(14)-O(2)-Cd(1) 114.5(2) C(14)-O(2)-H(2O) 111(3) Cd(1)-O(2)-H(2O) 122(3) N(2)-Cd(1)-N(1) 77.02(11) N(2)-Cd(1)-O(2) 71.97(11) N(1)-Cd(1)-O(2) 144.21(11) N(2)-Cd(1)-Cl(1) 152.95(8) N(1)-Cd(1)-Cl(1) 111.03(8) O(2)-Cd(1)-Cl(1) 90.16(8) N(2)-Cd(1)-Cl(2) 96.02(8) N(1)-Cd(1)-Cl(2) 105.94(8) O(2)-Cd(1)-Cl(2) 94.79(9) Cl(1)-Cd(1)-Cl(2) 105.81(4) Symmetry transformations used to generate equivalent atoms: Table E.34: Anisotropic displacement parameters (?2 x 103)for 7m_al7_a. The anisotropic displacement factor exponent takes the form: -2p2[ h2a*2U11 + ... + 2 h k a* b* U12 ] U11 U22 U33 U23 U13 C(1) 31(2) 33(2) 34(2) -12(2) -1(2) C(2) 42(3) 35(2) 37(2) -7(2) 6(2) C(3) 63(3) 55(3) 32(3) -12(2) 4(2) C(4) 87(4) 50(3) 44(3) -24(3) 14(3) C(5) 72(4) 43(3) 41(3) -21(2) 10(3) C(6) 32(2) 32(2) 32(2) -9(2) 6(2) C(7) 30(2) 34(2) 40(3) -7(2) -7(2) C(8) 40(3) 31(2) 32(2) -1(2) -10(2) C(9) 33(2) 27(2) 27(2) -10(2) -2(2) C(10) 51(3) 39(3) 29(2) -2(2) -4(2) C(11) 60(3) 47(3) 29(2) -1(2) 0(2) 40 Appendix E C(12) 52(3) 42(3) 34(3) -5(2) 10(2) C(13) 34(2) 39(2) 36(2) -9(2) 2(2) C(14) 37(2) 26(2) 26(2) -4(2) -1(2) C(15) 129(11) 180(14) 840(60) 170(20) -230(20) N(1) 28(2) 28(2) 31(2) -11(2) -1(2) N(2) 31(2) 23(2) 29(2) -6(2) -3(2) O(1) 30(2) 31(2) 43(2) -15(1) 0(1) O(2) 37(2) 32(2) 32(2) -2(2) 1(1) O(3) 361(17) 293(14) 340(16) -227(13) 221(14) Cl(1) 38(1) 25(1) 40(1) -3(1) -4(1) Cl(2) 47(1) 39(1) 60(1) -23(1) -13(1) Cd(1) 30(1) 28(1) 28(1) -2(1) -1(1) Table E.35: Torsion angles [?] for 7m_al7_a. O(1)-C(1)-C(2)-C(3) -179.9(4) C(6)-C(1)-C(2)-C(3) -56.8(5) C(1)-C(2)-C(3)-C(4) 55.9(5) C(2)-C(3)-C(4)-C(5) -55.9(6) C(3)-C(4)-C(5)-C(6) 57.2(6) C(4)-C(5)-C(6)-N(1) 179.8(4) C(4)-C(5)-C(6)-C(1) -58.0(5) O(1)-C(1)-C(6)-N(1) -54.1(4) C(2)-C(1)-C(6)-N(1) -178.3(3) O(1)-C(1)-C(6)-C(5) -177.9(3) C(2)-C(1)-C(6)-C(5) 57.9(5) N(1)-C(7)-C(8)-N(2) -61.7(4) N(2)-C(9)-C(10)-C(11) 178.1(3) C(14)-C(9)-C(10)-C(11) 55.3(5) C(9)-C(10)-C(11)-C(12) -54.2(5) C(10)-C(11)-C(12)-C(13) 54.8(5) C(11)-C(12)-C(13)-C(14) -57.6(5) C(12)-C(13)-C(14)-O(2) -176.4(3) C(12)-C(13)-C(14)-C(9) 59.2(4) N(2)-C(9)-C(14)-O(2) 51.0(4) C(10)-C(9)-C(14)-O(2) 176.6(3) N(2)-C(9)-C(14)-C(13) 176.5(3) C(10)-C(9)-C(14)-C(13) -57.9(4) C(8)-C(7)-N(1)-C(6) -177.4(3) C(8)-C(7)-N(1)-Cd(1) 45.9(4) C(5)-C(6)-N(1)-C(7) -77.4(4) C(1)-C(6)-N(1)-C(7) 159.7(3) C(5)-C(6)-N(1)-Cd(1) 49.6(4) C(1)-C(6)-N(1)-Cd(1) -73.3(4) C(7)-C(8)-N(2)-C(9) 167.6(3) 41 Appendix E C(7)-C(8)-N(2)-Cd(1) 41.0(4) C(14)-C(9)-N(2)-C(8) -169.9(3) C(10)-C(9)-N(2)-C(8) 66.6(4) C(14)-C(9)-N(2)-Cd(1) -45.4(3) C(10)-C(9)-N(2)-Cd(1) -168.9(3) C(13)-C(14)-O(2)-Cd(1) -156.7(3) C(9)-C(14)-O(2)-Cd(1) -32.3(4) C(8)-N(2)-Cd(1)-N(1) -12.4(2) C(9)-N(2)-Cd(1)-N(1) -140.5(3) C(8)-N(2)-Cd(1)-O(2) 149.5(3) C(9)-N(2)-Cd(1)-O(2) 21.4(2) C(8)-N(2)-Cd(1)-Cl(1) 98.6(3) C(9)-N(2)-Cd(1)-Cl(1) -29.4(4) C(8)-N(2)-Cd(1)-Cl(2) -117.4(2) C(9)-N(2)-Cd(1)-Cl(2) 114.5(2) C(7)-N(1)-Cd(1)-N(2) -17.4(2) C(6)-N(1)-Cd(1)-N(2) -147.0(3) C(7)-N(1)-Cd(1)-O(2) -47.8(3) C(6)-N(1)-Cd(1)-O(2) -177.3(2) C(7)-N(1)-Cd(1)-Cl(1) -170.4(2) C(6)-N(1)-Cd(1)-Cl(1) 60.1(3) C(7)-N(1)-Cd(1)-Cl(2) 75.2(2) C(6)-N(1)-Cd(1)-Cl(2) -54.3(3) C(14)-O(2)-Cd(1)-N(2) 6.4(2) C(14)-O(2)-Cd(1)-N(1) 37.5(4) C(14)-O(2)-Cd(1)-Cl(1) 165.7(3) C(14)-O(2)-Cd(1)-Cl(2) -88.4(3) Symmetry transformations used to generate equivalent atoms: Table E.36: Hydrogen bonds for 7m_al7_a [? and ?]. D-H...A d(D-H) d(H...A) d(D...A) <(DHA) O(2)-H(2O)...O(1)#1 0.75(4) 1.95(5) 2.702(4) 172(5) Symmetry transformations used to generate equivalent atoms: #1 -x,-y,-z+1 42 Appendix E BHEEN/Cd Data Figure E.7: The cadmium(II) complex of BHEEN and the labelling scheme used Table E.37: Crystal data and structure refinement for 8m_alv4_0a. Identification code 8m_alv4_0a Empirical formula C12 H32 Cd2 Cl4 N4 O4 Formula weight 663.02 Temperature 173(2) K Wavelength 0.71073 ? Crystal system Orthorhombic Space group Pbca Unit cell dimensions a = 11.0918(3) ? ? = 90?. b = 12.4205(3) ? ? = 90?. c = 15.9911(4) ? ? = 90?. Volume 2203.03(10) ? 3 Z 4 Density (calculated) 1.999 Mg/m 3 Absorption coefficient 2.440 mm -1 F(000) 1312 Crystal size 0.28 x 0.18 x 0.04 mm 3 Theta range for data collection 2.55 to 27.99?. Index ranges -13<=h<=14, -14<=k<=16, -20<=l<=21 Reflections collected 25373 Independent reflections 2659 [R(int) = 0.0626] Completeness to theta = 27.99? 100.0 % Absorption correction Integration Max. and min. transmission 0.9087 and 0.5482 Refinement method Full-matrix least-squares on F 2 43 Appendix E Data / restraints / parameters 2659 / 0 / 126 Goodness-of-fit on F 2 0.956 Final R indices [I>2?(I)] R1 = 0.0222, wR2 = 0.0498 R indices (all data) R1 = 0.0301, wR2 = 0.0521 Largest diff. peak and hole 1.206 and -0.406 e.? -3 Table E.38: Atomic coordinates ( x 104) and equivalent isotropic displacement parameters (?2x 103) for 8m_alv4_0a. U(eq) is defined as one third of the trace of the orthogonalized Uij tensor. x y z U(eq) C(1) 8634(2) 2592(2) -1204(1) 22(1) C(2) 7515(2) 1918(2) -1080(1) 20(1) C(3) 6392(2) 957(2) 44(1) 19(1) C(4) 6449(2) 743(2) 974(1) 21(1) C(5) 7749(2) 272(2) 2145(1) 20(1) C(6) 8989(2) -62(2) 2422(1) 23(1) N(1) 7300(1) 1777(2) -182(1) 16(1) N(2) 7634(1) 296(2) 1226(1) 16(1) O(1) 9664(1) 2114(1) -810(1) 20(1) O(2) 9244(2) -1134(2) 2146(1) 28(1) Cd(1) 9070(1) 1272(1) 479(1) 16(1) Cl(1) 11172(1) 617(1) 611(1) 21(1) Cl(2) 9058(1) 2912(1) 1437(1) 23(1) Table E.39: Bond lengths [?] and angles [?] for 8m_alv4_0a. C(1)-O(1) 1.433(3) C(1)-C(2) 1.510(3) C(1)-H(1A) 0.9900 C(1)-H(1B) 0.9900 C(2)-N(1) 1.466(3) C(2)-H(2A) 0.9900 C(2)-H(2B) 0.9900 C(3)-N(1) 1.477(3) C(3)-C(4) 1.511(3) C(3)-H(3A) 0.9900 C(3)-H(3B) 0.9900 C(4)-N(2) 1.482(2) C(4)-H(4A) 0.9900 C(4)-H(4B) 0.9900 C(5)-N(2) 1.476(2) 44 Appendix E C(5)-C(6) 1.503(3) C(5)-H(5A) 0.9900 C(5)-H(5B) 0.9900 C(6)-O(2) 1.431(3) C(6)-H(6A) 0.9900 C(6)-H(6B) 0.9900 N(1)-Cd(1) 2.3172(16) N(1)-H(1N) 0.9300 N(2)-Cd(1) 2.3312(16) N(2)-H(2N) 0.9300 O(1)-Cd(1) 2.4030(16) O(1)-H(1O) 0.76(3) O(2)-H(2O) 0.77(3) Cd(1)-Cl(1) 2.4782(5) Cd(1)-Cl(2) 2.5486(6) Cd(1)-Cl(1)#1 2.9353(6) Cl(1)-Cd(1)#1 2.9353(6) O(1)-C(1)-C(2) 111.63(18) O(1)-C(1)-H(1A) 109.3 C(2)-C(1)-H(1A) 109.3 O(1)-C(1)-H(1B) 109.3 C(2)-C(1)-H(1B) 109.3 H(1A)-C(1)-H(1B) 108.0 N(1)-C(2)-C(1) 109.15(17) N(1)-C(2)-H(2A) 109.9 C(1)-C(2)-H(2A) 109.9 N(1)-C(2)-H(2B) 109.9 C(1)-C(2)-H(2B) 109.9 H(2A)-C(2)-H(2B) 108.3 N(1)-C(3)-C(4) 109.49(16) N(1)-C(3)-H(3A) 109.8 C(4)-C(3)-H(3A) 109.8 N(1)-C(3)-H(3B) 109.8 C(4)-C(3)-H(3B) 109.8 H(3A)-C(3)-H(3B) 108.2 N(2)-C(4)-C(3) 111.73(16) N(2)-C(4)-H(4A) 109.3 C(3)-C(4)-H(4A) 109.3 N(2)-C(4)-H(4B) 109.3 C(3)-C(4)-H(4B) 109.3 H(4A)-C(4)-H(4B) 107.9 N(2)-C(5)-C(6) 112.22(16) N(2)-C(5)-H(5A) 109.2 C(6)-C(5)-H(5A) 109.2 N(2)-C(5)-H(5B) 109.2 45 Appendix E C(6)-C(5)-H(5B) 109.2 H(5A)-C(5)-H(5B) 107.9 O(2)-C(6)-C(5) 110.30(18) O(2)-C(6)-H(6A) 109.6 C(5)-C(6)-H(6A) 109.6 O(2)-C(6)-H(6B) 109.6 C(5)-C(6)-H(6B) 109.6 H(6A)-C(6)-H(6B) 108.1 C(2)-N(1)-C(3) 115.67(16) C(2)-N(1)-Cd(1) 109.97(12) C(3)-N(1)-Cd(1) 106.20(12) C(2)-N(1)-H(1N) 108.3 C(3)-N(1)-H(1N) 108.3 Cd(1)-N(1)-H(1N) 108.3 C(5)-N(2)-C(4) 110.81(15) C(5)-N(2)-Cd(1) 117.50(12) C(4)-N(2)-Cd(1) 105.78(12) C(5)-N(2)-H(2N) 107.4 C(4)-N(2)-H(2N) 107.4 Cd(1)-N(2)-H(2N) 107.4 C(1)-O(1)-Cd(1) 109.81(12) C(1)-O(1)-H(1O) 108.4(19) Cd(1)-O(1)-H(1O) 116(2) C(6)-O(2)-H(2O) 112(2) N(1)-Cd(1)-N(2) 78.17(6) N(1)-Cd(1)-O(1) 73.92(6) N(2)-Cd(1)-O(1) 148.52(5) N(1)-Cd(1)-Cl(1) 157.67(4) N(2)-Cd(1)-Cl(1) 115.41(4) O(1)-Cd(1)-Cl(1) 87.59(4) N(1)-Cd(1)-Cl(2) 93.07(5) N(2)-Cd(1)-Cl(2) 95.96(4) O(1)-Cd(1)-Cl(2) 99.74(4) Cl(1)-Cd(1)-Cl(2) 102.493(18) N(1)-Cd(1)-Cl(1)#1 82.39(5) N(2)-Cd(1)-Cl(1)#1 79.96(4) O(1)-Cd(1)-Cl(1)#1 82.19(4) Cl(1)-Cd(1)-Cl(1)#1 82.786(17) Cl(2)-Cd(1)-Cl(1)#1 174.407(15) Cd(1)-Cl(1)-Cd(1)#1 97.214(17) _____________________________________________________________ Symmetry transformations used to generate equivalent atoms: #1 -x+2,-y,-z 46 Appendix E Table E.40: Anisotropic displacement parameters (?2x 103)for 8m_alv4_0a. The anisotropic displacement factor exponent takes the form: -2p2[ h2a*2U11 + ... + 2 h k a* b* U12 ] U11 U22 U33 U23 U13 U12 C(1) 28(1) 16(1) 23(1) 4(1) 1(1) 5(1) C(2) 23(1) 19(1) 18(1) -1(1) -4(1) 4(1) C(3) 14(1) 19(1) 23(1) -1(1) -5(1) 2(1) C(4) 13(1) 23(1) 26(1) 2(1) 0(1) 2(1) C(5) 20(1) 23(1) 18(1) 0(1) 1(1) 1(1) C(6) 22(1) 28(1) 19(1) 2(1) -1(1) 0(1) N(1) 18(1) 14(1) 17(1) -2(1) -2(1) 1(1) N(2) 14(1) 15(1) 18(1) -1(1) 1(1) 2(1) O(1) 22(1) 19(1) 20(1) 0(1) 1(1) 3(1) O(2) 29(1) 32(1) 23(1) 2(1) -3(1) 11(1) Cd(1) 13(1) 18(1) 17(1) 1(1) -1(1) 0(1) Cl(1) 15(1) 19(1) 29(1) -4(1) -2(1) 2(1) Cl(2) 25(1) 21(1) 23(1) -6(1) 0(1) -2(1) Table E.41: Torsion angles [?] for 8m_alv4_0a. O(1)-C(1)-C(2)-N(1) 57.5(2) N(1)-C(3)-C(4)-N(2) -62.6(2) N(2)-C(5)-C(6)-O(2) -62.4(2) C(1)-C(2)-N(1)-C(3) -167.83(18) C(1)-C(2)-N(1)-Cd(1) -47.6(2) C(4)-C(3)-N(1)-C(2) 168.63(17) C(4)-C(3)-N(1)-Cd(1) 46.34(18) C(6)-C(5)-N(2)-C(4) -173.70(18) C(6)-C(5)-N(2)-Cd(1) -52.0(2) C(3)-C(4)-N(2)-C(5) 170.11(18) C(3)-C(4)-N(2)-Cd(1) 41.7(2) C(2)-C(1)-O(1)-Cd(1) -36.4(2) C(2)-N(1)-Cd(1)-N(2) -144.06(15) C(3)-N(1)-Cd(1)-N(2) -18.22(12) C(2)-N(1)-Cd(1)-O(1) 21.23(13) C(3)-N(1)-Cd(1)-O(1) 147.07(14) C(2)-N(1)-Cd(1)-Cl(1) -14.0(2) C(3)-N(1)-Cd(1)-Cl(1) 111.86(14) C(2)-N(1)-Cd(1)-Cl(2) 120.49(13) C(3)-N(1)-Cd(1)-Cl(2) -113.67(12) C(2)-N(1)-Cd(1)-Cl(1)#1 -62.79(13) C(3)-N(1)-Cd(1)-Cl(1)#1 63.05(12) C(5)-N(2)-Cd(1)-N(1) -136.35(15) C(4)-N(2)-Cd(1)-N(1) -12.07(13) 47 Appendix E C(5)-N(2)-Cd(1)-O(1) -164.21(13) C(4)-N(2)-Cd(1)-O(1) -39.93(19) C(5)-N(2)-Cd(1)-Cl(1) 62.42(15) C(4)-N(2)-Cd(1)-Cl(1) -173.30(12) C(5)-N(2)-Cd(1)-Cl(2) -44.46(14) C(4)-N(2)-Cd(1)-Cl(2) 79.82(13) C(5)-N(2)-Cd(1)-Cl(1)#1 139.40(14) C(4)-N(2)-Cd(1)-Cl(1)#1 -96.32(13) C(1)-O(1)-Cd(1)-N(1) 8.30(13) C(1)-O(1)-Cd(1)-N(2) 36.7(2) C(1)-O(1)-Cd(1)-Cl(1) 175.64(14) C(1)-O(1)-Cd(1)-Cl(2) -82.10(13) C(1)-O(1)-Cd(1)-Cl(1)#1 92.59(13) N(1)-Cd(1)-Cl(1)-Cd(1)#1 -48.75(13) N(2)-Cd(1)-Cl(1)-Cd(1)#1 75.24(5) O(1)-Cd(1)-Cl(1)-Cd(1)#1 -82.43(4) Cl(2)-Cd(1)-Cl(1)-Cd(1)#1 178.122(18) Cl(1)#1-Cd(1)-Cl(1)-Cd(1)#1 0.0 Symmetry transformations used to generate equivalent atoms: #1 -x+2,-y,-z Table E.42: Hydrogen bonds for 8m_alv4_0a [? and ?]. D-H...A d(D-H) d(H...A) d(D...A) <(DHA) O(1)-H(1O)...O(2)#1 0.76(3) 2.00(3) 2.741(2) 165(3) O(2)-H(2O)...Cl(2)#2 0.77(3) 2.41(3) 3.1756(18) 169(3) Symmetry transformations used to generate equivalent atoms: #1 -x+2,-y,-z #2 -x+2,y-1/2,-z+1/2 48 Appendix E BHEEN/Zn Data Figure E.8: The Zinc complex of BHEEN and the labelling scheme used Table E.43: Crystal data and structure refinement for 8m_alv22_0a. Identification code 8m_alv22_0a Empirical formula C12 H32 Cl2 N4 O4 Zn Formula weight 432.69 Temperature 173(2) K Wavelength 0.71073 ? Crystal system Monoclinic Space group P2(1)/c Unit cell dimensions a = 15.3169(2) ? ? = 90?. b = 8.98000(10) ? ? = 105.2260(10)?. c = 14.3231(2) ? ? = 90?. Volume 1900.93(4) ? 3 Z 4 Density (calculated) 1.512 Mg/m 3 Absorption coefficient 1.596 mm -1 F(000) 912 Crystal size 0.33 x 0.28 x 0.22 mm 3 Theta range for data collection 1.38 to 28.00?. Index ranges -20<=h<=20, -11<=k<=11, -18<=l<=18 Reflections collected 39686 Independent reflections 4588 [R(int) = 0.0422] Completeness to theta = 28.00? 100.0 % Absorption correction Integration Max. and min. transmission 0.7204 and 0.6210 49 Appendix E Refinement method Full-matrix least-squares on F 2 Data / restraints / parameters 4588 / 0 / 212 Goodness-of-fit on F 2 1.042 Final R indices [I>2?(I)] R1 = 0.0211, wR2 = 0.0546 R indices (all data) R1 = 0.0247, wR2 = 0.0556 Largest diff. peak and hole 0.321 and -0.440 e.? -3 Table E.44: Atomic coordinates ( x 104) and equivalent isotropic displacement parameters (?2x 103) for 8m_alv22_0a. U(eq) is defined as one third of the trace of the orthogonalized Uij tensor. x y z U(eq) C(1) 9151(1) 6684(2) 9108(1) 25(1) C(2) 8776(1) 5199(2) 9296(1) 24(1) C(3) 8449(1) 2681(1) 8648(1) 27(1) C(4) 8039(1) 1799(1) 7745(1) 30(1) C(5) 6807(1) 1859(2) 6240(1) 33(1) C(6) 5908(1) 2559(2) 5786(1) 35(1) C(7) 8951(1) 4943(1) 5752(1) 26(1) C(8) 8036(1) 5658(2) 5422(1) 23(1) C(9) 6942(1) 7224(1) 5946(1) 23(1) C(10) 6576(1) 7603(1) 6803(1) 22(1) C(11) 6234(1) 6605(1) 8244(1) 22(1) C(12) 5933(1) 5249(1) 8695(1) 24(1) N(1) 8565(1) 4268(1) 8410(1) 21(1) N(2) 7195(1) 2547(1) 7198(1) 22(1) N(3) 7746(1) 6246(1) 6263(1) 18(1) N(4) 6414(1) 6229(1) 7305(1) 18(1) O(1) 8469(1) 7510(1) 8446(1) 28(1) O(2) 6002(1) 4106(1) 5632(1) 36(1) O(3) 8882(1) 3653(1) 6303(1) 35(1) O(4) 6645(1) 4188(1) 8899(1) 26(1) Zn(1) 7465(1) 4796(1) 7271(1) 18(1) Cl(1) 9388(1) 8792(1) 6950(1) 30(1) Cl(2) 5882(1) 1011(1) 8455(1) 28(1) 50 Appendix E Table E.45: Bond lengths [?] and angles [?] for 8m_alv22_0a. C(1)-O(1) 1.4226(15) C(1)-C(2) 1.5041(18) C(1)-H(1A) 0.9900 C(1)-H(1B) 0.9900 C(2)-N(1) 1.4822(16) C(2)-H(2A) 0.9900 C(2)-H(2B) 0.9900 C(3)-N(1) 1.4861(15) C(3)-C(4) 1.5060(19) C(3)-H(3A) 0.9900 C(3)-H(3B) 0.9900 C(4)-N(2) 1.4839(17) C(4)-H(4A) 0.9900 C(4)-H(4B) 0.9900 C(5)-N(2) 1.4799(16) C(5)-C(6) 1.498(2) C(5)-H(5A) 0.9900 C(5)-H(5B) 0.9900 C(6)-O(2) 1.4198(17) C(6)-H(6A) 0.9900 C(6)-H(6B) 0.9900 C(7)-O(3) 1.4210(16) C(7)-C(8) 1.5006(19) C(7)-H(7A) 0.9900 C(7)-H(7B) 0.9900 C(8)-N(3) 1.4854(15) C(8)-H(8A) 0.9900 C(8)-H(8B) 0.9900 C(9)-N(3) 1.4840(15) C(9)-C(10) 1.5152(17) C(9)-H(9A) 0.9900 C(9)-H(9B) 0.9900 C(10)-N(4) 1.4814(14) C(10)-H(10A) 0.9900 C(10)-H(10B) 0.9900 C(11)-N(4) 1.4811(15) C(11)-C(12) 1.5061(17) C(11)-H(11A) 0.9900 C(11)-H(11B) 0.9900 C(12)-O(4) 1.4195(15) C(12)-H(12A) 0.9900 C(12)-H(12B) 0.9900 N(1)-Zn(1) 2.0683(10) N(1)-H(1N) 0.9300 N(2)-Zn(1) 2.0584(10) 51 Appendix E N(2)-H(2N) 0.9300 N(3)-Zn(1) 2.0711(10) N(3)-H(3N) 0.9300 N(4)-Zn(1) 2.0719(10) N(4)-H(4N) 0.9300 O(1)-H(1O) 0.8400 O(2)-H(2O) 0.8400 O(3)-H(3O) 0.8400 O(4)-H(4O) 0.8400 O(1)-C(1)-C(2) 109.44(10) O(1)-C(1)-H(1A) 109.8 C(2)-C(1)-H(1A) 109.8 O(1)-C(1)-H(1B) 109.8 C(2)-C(1)-H(1B) 109.8 H(1A)-C(1)-H(1B) 108.2 N(1)-C(2)-C(1) 110.81(10) N(1)-C(2)-H(2A) 109.5 C(1)-C(2)-H(2A) 109.5 N(1)-C(2)-H(2B) 109.5 C(1)-C(2)-H(2B) 109.5 H(2A)-C(2)-H(2B) 108.1 N(1)-C(3)-C(4) 110.82(11) N(1)-C(3)-H(3A) 109.5 C(4)-C(3)-H(3A) 109.5 N(1)-C(3)-H(3B) 109.5 C(4)-C(3)-H(3B) 109.5 H(3A)-C(3)-H(3B) 108.1 N(2)-C(4)-C(3) 108.91(10) N(2)-C(4)-H(4A) 109.9 C(3)-C(4)-H(4A) 109.9 N(2)-C(4)-H(4B) 109.9 C(3)-C(4)-H(4B) 109.9 H(4A)-C(4)-H(4B) 108.3 N(2)-C(5)-C(6) 109.09(11) N(2)-C(5)-H(5A) 109.9 C(6)-C(5)-H(5A) 109.9 N(2)-C(5)-H(5B) 109.9 C(6)-C(5)-H(5B) 109.9 H(5A)-C(5)-H(5B) 108.3 O(2)-C(6)-C(5) 111.07(11) O(2)-C(6)-H(6A) 109.4 C(5)-C(6)-H(6A) 109.4 O(2)-C(6)-H(6B) 109.4 C(5)-C(6)-H(6B) 109.4 H(6A)-C(6)-H(6B) 108.0 52 Appendix E O(3)-C(7)-C(8) 108.88(11) O(3)-C(7)-H(7A) 109.9 C(8)-C(7)-H(7A) 109.9 O(3)-C(7)-H(7B) 109.9 C(8)-C(7)-H(7B) 109.9 H(7A)-C(7)-H(7B) 108.3 N(3)-C(8)-C(7) 110.49(10) N(3)-C(8)-H(8A) 109.6 C(7)-C(8)-H(8A) 109.6 N(3)-C(8)-H(8B) 109.6 C(7)-C(8)-H(8B) 109.6 H(8A)-C(8)-H(8B) 108.1 N(3)-C(9)-C(10) 109.85(10) N(3)-C(9)-H(9A) 109.7 C(10)-C(9)-H(9A) 109.7 N(3)-C(9)-H(9B) 109.7 C(10)-C(9)-H(9B) 109.7 H(9A)-C(9)-H(9B) 108.2 N(4)-C(10)-C(9) 110.52(10) N(4)-C(10)-H(10A) 109.5 C(9)-C(10)-H(10A) 109.5 N(4)-C(10)-H(10B) 109.5 C(9)-C(10)-H(10B) 109.5 H(10A)-C(10)-H(10B) 108.1 N(4)-C(11)-C(12) 110.85(10) N(4)-C(11)-H(11A) 109.5 C(12)-C(11)-H(11A) 109.5 N(4)-C(11)-H(11B) 109.5 C(12)-C(11)-H(11B) 109.5 H(11A)-C(11)-H(11B) 108.1 O(4)-C(12)-C(11) 109.00(10) O(4)-C(12)-H(12A) 109.9 C(11)-C(12)-H(12A) 109.9 O(4)-C(12)-H(12B) 109.9 C(11)-C(12)-H(12B) 109.9 H(12A)-C(12)-H(12B) 108.3 C(2)-N(1)-C(3) 110.91(10) C(2)-N(1)-Zn(1) 119.67(8) C(3)-N(1)-Zn(1) 106.23(8) C(2)-N(1)-H(1N) 106.4 C(3)-N(1)-H(1N) 106.4 Zn(1)-N(1)-H(1N) 106.4 C(5)-N(2)-C(4) 112.48(10) C(5)-N(2)-Zn(1) 118.88(8) C(4)-N(2)-Zn(1) 106.38(8) C(5)-N(2)-H(2N) 106.1 53 Appendix E C(4)-N(2)-H(2N) 106.1 Zn(1)-N(2)-H(2N) 106.1 C(9)-N(3)-C(8) 111.28(9) C(9)-N(3)-Zn(1) 106.09(7) C(8)-N(3)-Zn(1) 120.16(8) C(9)-N(3)-H(3N) 106.1 C(8)-N(3)-H(3N) 106.1 Zn(1)-N(3)-H(3N) 106.1 C(11)-N(4)-C(10) 110.21(9) C(11)-N(4)-Zn(1) 119.59(8) C(10)-N(4)-Zn(1) 105.99(7) C(11)-N(4)-H(4N) 106.8 C(10)-N(4)-H(4N) 106.8 Zn(1)-N(4)-H(4N) 106.8 C(1)-O(1)-H(1O) 109.5 C(6)-O(2)-H(2O) 109.5 C(7)-O(3)-H(3O) 109.5 C(12)-O(4)-H(4O) 109.5 N(2)-Zn(1)-N(1) 85.76(4) N(2)-Zn(1)-N(3) 131.09(4) N(1)-Zn(1)-N(3) 114.76(4) N(2)-Zn(1)-N(4) 117.60(4) N(1)-Zn(1)-N(4) 126.92(4) N(3)-Zn(1)-N(4) 86.05(4) Symmetry transformations used to generate equivalent atoms: Table E.46: Anisotropic displacement parameters (?2x 103)for 8m_alv22_0a. The anisotropic displacement factor exponent takes the form: -2p2[ h2a*2U11 + ... + 2 h k a* b* U12 ] U11 U22 U33 U23 U13 U12 C(1) 18(1) 34(1) 23(1) -3(1) 2(1) 0(1) C(2) 18(1) 36(1) 17(1) 2(1) 3(1) 1(1) C(3) 24(1) 26(1) 32(1) 13(1) 8(1) 7(1) C(4) 35(1) 17(1) 41(1) 5(1) 18(1) 5(1) C(5) 53(1) 23(1) 27(1) -9(1) 16(1) -10(1) C(6) 37(1) 47(1) 24(1) -10(1) 13(1) -22(1) C(7) 25(1) 30(1) 26(1) -4(1) 14(1) -4(1) C(8) 25(1) 30(1) 16(1) 0(1) 9(1) -3(1) C(9) 23(1) 24(1) 21(1) 7(1) 5(1) 3(1) C(10) 22(1) 18(1) 26(1) 5(1) 8(1) 4(1) C(11) 21(1) 24(1) 23(1) -2(1) 10(1) 2(1) C(12) 20(1) 29(1) 24(1) 3(1) 10(1) 3(1) N(1) 19(1) 23(1) 22(1) 4(1) 8(1) 2(1) 54 Appendix E N(2) 27(1) 21(1) 22(1) -2(1) 12(1) -2(1) N(3) 18(1) 21(1) 15(1) 0(1) 5(1) 0(1) N(4) 17(1) 20(1) 18(1) 0(1) 5(1) -1(1) O(1) 22(1) 37(1) 25(1) 4(1) 6(1) 4(1) O(2) 45(1) 37(1) 25(1) -8(1) 8(1) -1(1) O(3) 32(1) 31(1) 42(1) 7(1) 9(1) 2(1) O(4) 22(1) 25(1) 33(1) 4(1) 9(1) 3(1) Zn(1) 22(1) 16(1) 17(1) 2(1) 6(1) 3(1) Cl(1) 25(1) 32(1) 33(1) -2(1) 11(1) -7(1) Cl(2) 26(1) 32(1) 25(1) 2(1) 7(1) -5(1) Table E.47: Torsion angles [?] for 8m_alv22_0a. O(1)-C(1)-C(2)-N(1) 66.45(13) N(1)-C(3)-C(4)-N(2) -53.10(14) N(2)-C(5)-C(6)-O(2) 61.98(14) O(3)-C(7)-C(8)-N(3) 66.35(13) N(3)-C(9)-C(10)-N(4) -53.11(13) N(4)-C(11)-C(12)-O(4) 63.23(14) C(1)-C(2)-N(1)-C(3) 163.69(10) C(1)-C(2)-N(1)-Zn(1) -72.11(12) C(4)-C(3)-N(1)-C(2) 167.57(10) C(4)-C(3)-N(1)-Zn(1) 36.03(12) C(6)-C(5)-N(2)-C(4) 173.53(11) C(6)-C(5)-N(2)-Zn(1) -61.24(13) C(3)-C(4)-N(2)-C(5) 172.89(10) C(3)-C(4)-N(2)-Zn(1) 41.10(11) C(10)-C(9)-N(3)-C(8) 170.99(10) C(10)-C(9)-N(3)-Zn(1) 38.65(11) C(7)-C(8)-N(3)-C(9) 168.18(10) C(7)-C(8)-N(3)-Zn(1) -67.04(12) C(12)-C(11)-N(4)-C(10) 171.58(10) C(12)-C(11)-N(4)-Zn(1) -65.29(12) C(9)-C(10)-N(4)-C(11) 168.68(10) C(9)-C(10)-N(4)-Zn(1) 37.93(11) C(5)-N(2)-Zn(1)-N(1) -145.20(10) C(4)-N(2)-Zn(1)-N(1) -17.08(8) C(5)-N(2)-Zn(1)-N(3) -25.70(12) C(4)-N(2)-Zn(1)-N(3) 102.42(8) C(5)-N(2)-Zn(1)-N(4) 84.95(10) C(4)-N(2)-Zn(1)-N(4) -146.93(7) C(2)-N(1)-Zn(1)-N(2) -136.55(9) C(3)-N(1)-Zn(1)-N(2) -10.12(8) C(2)-N(1)-Zn(1)-N(3) 89.71(9) 55 Appendix E C(3)-N(1)-Zn(1)-N(3) -143.87(7) C(2)-N(1)-Zn(1)-N(4) -14.86(10) C(3)-N(1)-Zn(1)-N(4) 111.56(8) C(9)-N(3)-Zn(1)-N(2) 109.62(8) C(8)-N(3)-Zn(1)-N(2) -17.57(11) C(9)-N(3)-Zn(1)-N(1) -143.28(7) C(8)-N(3)-Zn(1)-N(1) 89.52(9) C(9)-N(3)-Zn(1)-N(4) -14.15(8) C(8)-N(3)-Zn(1)-N(4) -141.34(9) C(11)-N(4)-Zn(1)-N(2) 86.90(9) C(10)-N(4)-Zn(1)-N(2) -147.93(7) C(11)-N(4)-Zn(1)-N(1) -19.85(10) C(10)-N(4)-Zn(1)-N(1) 105.31(8) C(11)-N(4)-Zn(1)-N(3) -138.09(9) C(10)-N(4)-Zn(1)-N(3) -12.92(7) Symmetry transformations used to generate equivalent atoms: Table E.48: Hydrogen bonds for 8m_alv22_0a [? and ?]. D-H...A d(D-H) d(H...A) d(D...A) <(DHA) N(4)-H(4N)...O(2) 0.93 2.44 2.9961(13) 119 O(1)-H(1O)...Cl(1) 0.84 2.25 3.0789(10) 167 O(2)-H(2O)...Cl(2)#1 0.84 2.26 3.0775(10) 164 O(3)-H(3O)...Cl(1)#2 0.84 2.32 3.1330(11) 164 O(4)-H(4O)...Cl(2) 0.84 2.25 3.0846(10) 171 Symmetry transformations used to generate equivalent atoms: #1 x,-y+1/2,z-1/2 #2 -x+2,y-1/2,-z+3/2 56 Appendix E Imidazolinium Salt (1) Data Figure E.9: The Imidazolinium Salt 1 and the labelling scheme used Table E.49: Crystal data and structure refinement for 7m_al11_0s. Identification code 7m_al11_0s Empirical formula C15 H27 N3 O5 Formula weight 329.40 Temperature 273(2) K Wavelength 0.71073 ? Crystal system Orthorhombic Space group C222(1) Unit cell dimensions a = 7.0296(2) ? ? = 90?. b = 9.8263(2) ? ? = 90?. c = 25.1764(6) ? ? = 90?. Volume 1739.06(7) ?3 Z 4 Density (calculated) 1.258 Mg/m3 Absorption coefficient 0.094 mm-1 F(000) 712 Crystal size 0.45 x 0.29 x 0.16 mm3 Theta range for data collection 1.62 to 28.29?. Index ranges -9?h?9, -13?k?11, -31?l?33 Reflections collected 10862 Independent reflections 1244 [R(int) = 0.0418] Completeness to theta = 28.29? 100.0 % Absorption correction None Max. and min. transmission 0.9850 and 0.9587 Refinement method Full-matrix least-squares on F2 Data / restraints / parameters 1244 / 0 / 120 Goodness-of-fit on F2 1.142 57 Appendix E Final R indices [I>2?(I)] R1 = 0.0370, wR2 = 0.0981 R indices (all data) R1 = 0.0400, wR2 = 0.1000 Absolute structure parameter -10(10) Largest diff. peak and hole 0.215 and -0.186 e.?-3 Table E.50: Atomic coordinates ( x 104) and equivalent isotropic displacement parameters (?2x 103) for 7m_al11_0s. U(eq) is defined as one third of the trace of the orthogonalized Uij tensor. x y z U(eq) N(1) 282(2) 2933(1) 2928(1) 24(1) N(2) 5000 2398(2) 2500 27(1) O(1) -2815(2) 4016(2) 3559(1) 48(1) O(2) 5816(2) 1769(2) 2863(1) 36(1) O(3) 5000 3651(2) 2500 62(1) C(1) -1273(3) 3304(2) 3792(1) 29(1) C(2) -971(3) 3888(2) 4348(1) 39(1) C(3) 753(4) 3264(3) 4617(1) 47(1) C(4) 2525(3) 3461(3) 4287(1) 52(1) C(5) 2259(3) 2858(3) 3732(1) 43(1) C(6) 531(2) 3490(2) 3464(1) 25(1) C(7) 235(2) 1464(2) 2799(1) 25(1) C(8) 0 3650(2) 2500 24(1) Table E.51: Bond lengths [?] and angles [?] for 7m_al11_0s. N(1)-C(8) 1.3026(17) N(1)-C(6) 1.4671(18) N(1)-C(7) 1.4796(19) N(2)-O(3) 1.231(3) N(2)-O(2)#1 1.2443(16) N(2)-O(2) 1.2443(16) O(1)-C(1) 1.418(2) O(1)-H(1A) 0.80(3) C(1)-C(6) 1.524(2) C(1)-C(2) 1.529(2) C(1)-H(1) 0.9800 C(2)-C(3) 1.516(3) C(2)-H(2A) 0.9700 C(2)-H(2B) 0.9700 C(3)-C(4) 1.509(3) C(3)-H(3A) 0.9700 C(3)-H(3B) 0.9700 C(4)-C(5) 1.530(3) 58 Appendix E C(4)-H(4A) 0.9700 C(4)-H(4B) 0.9700 C(5)-C(6) 1.521(2) C(5)-H(5A) 0.9700 C(5)-H(5B) 0.9700 C(6)-H(6) 0.9800 C(7)-C(7)#2 1.541(3) C(7)-H(7A) 0.97(2) C(7)-H(7B) 0.94(3) C(8)-N(1)#2 1.3026(16) C(8)-H(8) 0.93(3) C(8)-N(1)-C(6) 125.25(13) C(8)-N(1)-C(7) 110.05(13) C(6)-N(1)-C(7) 124.65(12) O(3)-N(2)-O(2)#1 119.78(10) O(3)-N(2)-O(2) 119.78(10) O(2)#1-N(2)-O(2) 120.4(2) C(1)-O(1)-H(1A) 106(3) O(1)-C(1)-C(6) 110.66(14) O(1)-C(1)-C(2) 107.49(16) C(6)-C(1)-C(2) 109.61(14) O(1)-C(1)-H(1) 109.7 C(6)-C(1)-H(1) 109.7 C(2)-C(1)-H(1) 109.7 C(3)-C(2)-C(1) 111.57(16) C(3)-C(2)-H(2A) 109.3 C(1)-C(2)-H(2A) 109.3 C(3)-C(2)-H(2B) 109.3 C(1)-C(2)-H(2B) 109.3 H(2A)-C(2)-H(2B) 108.0 C(4)-C(3)-C(2) 111.26(16) C(4)-C(3)-H(3A) 109.4 C(2)-C(3)-H(3A) 109.4 C(4)-C(3)-H(3B) 109.4 C(2)-C(3)-H(3B) 109.4 H(3A)-C(3)-H(3B) 108.0 C(3)-C(4)-C(5) 110.61(19) C(3)-C(4)-H(4A) 109.5 C(5)-C(4)-H(4A) 109.5 C(3)-C(4)-H(4B) 109.5 C(5)-C(4)-H(4B) 109.5 H(4A)-C(4)-H(4B) 108.1 C(6)-C(5)-C(4) 110.14(17) C(6)-C(5)-H(5A) 109.6 C(4)-C(5)-H(5A) 109.6 59 Appendix E C(6)-C(5)-H(5B) 109.6 C(4)-C(5)-H(5B) 109.6 H(5A)-C(5)-H(5B) 108.1 N(1)-C(6)-C(5) 110.50(14) N(1)-C(6)-C(1) 110.74(13) C(5)-C(6)-C(1) 112.08(13) N(1)-C(6)-H(6) 107.8 C(5)-C(6)-H(6) 107.8 C(1)-C(6)-H(6) 107.8 N(1)-C(7)-C(7)#2 102.66(8) N(1)-C(7)-H(7A) 110.5(12) C(7)#2-C(7)-H(7A) 113.4(12) N(1)-C(7)-H(7B) 107.8(14) C(7)#2-C(7)-H(7B) 113.5(14) H(7A)-C(7)-H(7B) 108.7(17) N(1)#2-C(8)-N(1) 114.48(19) N(1)#2-C(8)-H(8) 122.76(9) N(1)-C(8)-H(8) 122.76(9) Symmetry transformations used to generate equivalent atoms: #1 -x+1,y,-z+1/2 #2 -x,y,-z+1/2 Table E.52: Anisotropic displacement parameters (?2x 103)for 7m_al11_0s. The anisotropic displacement factor exponent takes the form: -2p2[ h2a*2U11 + ... + 2 h k a* b* U12 ] U11 U22 U33 U23 U13 N(1) 34(1) 22(1) 16(1) -1(1) -1(1) N(2) 25(1) 24(1) 32(1) 0 5(1) O(1) 36(1) 63(1) 46(1) -21(1) -11(1) O(2) 35(1) 37(1) 36(1) 0(1) -7(1) O(3) 106(2) 20(1) 60(1) 0 4(2) C(1) 31(1) 33(1) 24(1) -3(1) 2(1) C(2) 44(1) 51(1) 21(1) -6(1) 5(1) C(3) 66(1) 59(1) 16(1) -1(1) -2(1) C(4) 42(1) 89(2) 26(1) -11(1) -14(1) C(5) 32(1) 73(1) 23(1) -9(1) -5(1) C(6) 32(1) 28(1) 15(1) -1(1) -1(1) C(7) 31(1) 22(1) 23(1) 1(1) 0(1) C(8) 29(1) 23(1) 19(1) 0 0(1) 60 Appendix E Table E.53: Torsion angles [?] for 7m_al11_0s. O(1)-C(1)-C(2)-C(3) -175.64(17) C(6)-C(1)-C(2)-C(3) -55.3(2) C(1)-C(2)-C(3)-C(4) 56.8(3) C(2)-C(3)-C(4)-C(5) -56.9(3) C(3)-C(4)-C(5)-C(6) 56.5(3) C(8)-N(1)-C(6)-C(5) -131.43(16) C(7)-N(1)-C(6)-C(5) 51.3(2) C(8)-N(1)-C(6)-C(1) 103.77(17) C(7)-N(1)-C(6)-C(1) -73.5(2) C(4)-C(5)-C(6)-N(1) 179.13(17) C(4)-C(5)-C(6)-C(1) -56.8(2) O(1)-C(1)-C(6)-N(1) -61.85(19) C(2)-C(1)-C(6)-N(1) 179.77(15) O(1)-C(1)-C(6)-C(5) 174.24(16) C(2)-C(1)-C(6)-C(5) 55.9(2) C(8)-N(1)-C(7)-C(7)#2 -2.6(2) C(6)-N(1)-C(7)-C(7)#2 175.03(16) C(6)-N(1)-C(8)-N(1)#2 -176.56(18) C(7)-N(1)-C(8)-N(1)#2 1.10(9) Symmetry transformations used to generate equivalent atoms: #1 -x+1,y,-z+1/2 #2 -x,y,-z+1/2 Table E.54: Hydrogen bonds for 7m_al11_0s [? and ?]. D-H...A d(D-H) d(H...A) d(D...A) <(DHA) O(1)-H(1A)...O(2)#3 0.80(3) 2.19(3) 2.977(2) 165(3) O(1)-H(1A)...O(3)#3 0.80(3) 2.44(3) 3.0969(16) 140(3) Symmetry transformations used to generate equivalent atoms: #1 -x+1,y,-z+1/2 #2 -x,y,-z+1/2 #3 x-1,y,z 61 Appendix E Z witterion (2) Data Figure E.10: The Zwitterion 2 and the labelling scheme used Table E.55: Crystal data and structure refinement for 8m_alv8_0ff. Identification code 8m_alv8_0ff Empirical formula C4 H12 N2 O4 Formula weight 152.16 Temperature 293(2) K Wavelength 0.71073 ? Crystal system Monoclinic Space group P2/c Unit cell dimensions a = 8.4164(3) ? ? = 90?. b = 5.9335(2) ? ? = 116.764(2)?. c = 15.6461(6) ? ? = 90?. Volume 697.64(4) ?3 Z 4 Density (calculated) 1.449 Mg/m3 Absorption coefficient 0.128 mm-1 F(000) 328 Crystal size 0.47 x 0.11 x 0.09 mm3 Theta range for data collection 2.71 to 28.33?. Index ranges -10?h?11, -7?k?7, -20?l?20 Reflections collected 9150 Independent reflections 1748 [R(int) = 0.0579] Completeness to theta = 28.33? 100.0 % Absorption correction None Max. and min. transmission 0.9886 and 0.9424 Refinement method Full-matrix least-squares on F2 Data / restraints / parameters 1748 / 0 / 120 Goodness-of-fit on F2 1.027 62 Appendix E Final R indices [I>2?(I)] R1 = 0.0458, wR2 = 0.1207 R indices (all data) R1 = 0.0682, wR2 = 0.1296 Largest diff. peak and hole 0.591 and -0.203 e.?-3 Table E.56: Atomic coordinates ( x 104) and equivalent isotropic displacement parameters (?2x 103) for 8m_alv8_0ff. U(eq) is defined as one third of the trace of the orthogonalized Uij tensor. x y z U(eq) C(1) 6350(2) 7346(3) 1400(1) 23(1) C(2) 7659(2) 8056(3) 1027(1) 23(1) C(3) 7215(2) 6873(3) 94(1) 24(1) C(4) 7663(2) 7100(3) 3165(1) 19(1) N(1) 6823(2) 8256(3) 2344(1) 23(1) N(2) 8430(2) 7582(3) -311(1) 21(1) O(1) 7611(2) 10400(2) 871(1) 33(1) O(2) 8031(2) 8078(2) 3949(1) 25(1) O(3) 8045(2) 5030(2) 3128(1) 23(1) O(4) 0 2601(3) 2500 27(1) O(5) 5000 2482(3) 2500 35(1) Table E.57: Bond lengths [?] and angles [?] for 8m_alv8_0ff. C(1)-N(1) 1.450(2) C(1)-C(2) 1.521(2) C(1)-H(1A) 0.9700 C(1)-H(1B) 0.9700 C(2)-O(1) 1.410(2) C(2)-C(3) 1.507(2) C(2)-H(2) 0.9800 C(3)-N(2) 1.485(2) C(3)-H(3A) 0.9700 C(3)-H(3B) 0.9700 C(4)-O(2) 1.262(2) C(4)-O(3) 1.2779(19) C(4)-N(1) 1.342(2) N(1)-H(1N) 0.83(2) N(2)-H(2N) 0.93(2) N(2)-H(3N) 0.90(3) N(2)-H(4N) 0.88(2) O(1)-H(1O) 1.03(4) O(4)-H(2O) 0.90(2) O(5)-H(4O) 0.85(2) 63 Appendix E N(1)-C(1)-C(2) 112.00(14) N(1)-C(1)-H(1A) 109.2 C(2)-C(1)-H(1A) 109.2 N(1)-C(1)-H(1B) 109.2 C(2)-C(1)-H(1B) 109.2 H(1A)-C(1)-H(1B) 107.9 O(1)-C(2)-C(3) 108.47(14) O(1)-C(2)-C(1) 111.74(15) C(3)-C(2)-C(1) 109.67(14) O(1)-C(2)-H(2) 109.0 C(3)-C(2)-H(2) 109.0 C(1)-C(2)-H(2) 109.0 N(2)-C(3)-C(2) 111.24(14) N(2)-C(3)-H(3A) 109.4 C(2)-C(3)-H(3A) 109.4 N(2)-C(3)-H(3B) 109.4 C(2)-C(3)-H(3B) 109.4 H(3A)-C(3)-H(3B) 108.0 O(2)-C(4)-O(3) 122.02(15) O(2)-C(4)-N(1) 119.19(15) O(3)-C(4)-N(1) 118.79(15) C(4)-N(1)-C(1) 124.72(16) C(4)-N(1)-H(1N) 115.6(14) C(1)-N(1)-H(1N) 119.5(14) C(3)-N(2)-H(2N) 110.7(12) C(3)-N(2)-H(3N) 110.8(14) H(2N)-N(2)-H(3N) 109.4(17) C(3)-N(2)-H(4N) 111.2(13) H(2N)-N(2)-H(4N) 105.6(18) H(3N)-N(2)-H(4N) 108.9(19) C(2)-O(1)-H(1O) 110.1(19) _____________________________________________________________ Symmetry transformations used to generate equivalent atoms: Table E.58: Anisotropic displacement parameters (?2x 103) for 8m_alv8_0ff. The anisotropic displacement factor exponent takes the form: -2p2[ h2a*2U11 + ... + 2 h k a* b* U12 ] U11 U22 U33 U23 U13 C(1) 22(1) 26(1) 17(1) 1(1) 7(1) C(2) 26(1) 23(1) 17(1) -1(1) 9(1) C(3) 28(1) 25(1) 21(1) -2(1) 12(1) C(4) 17(1) 22(1) 20(1) 0(1) 10(1) N(1) 30(1) 21(1) 21(1) 1(1) 13(1) N(2) 27(1) 20(1) 17(1) -2(1) 10(1) 64 Appendix E 65 O(1) 51(1) 24(1) 27(1) 1(1) 18(1) O(2) 29(1) 27(1) 19(1) -5(1) 10(1) O(3) 27(1) 19(1) 22(1) 2(1) 12(1) O(4) 33(1) 21(1) 34(1) 0 22(1) O(5) 28(1) 19(1) 53(1) 0 14(1) Table E.59: Torsion angles [?] for 8m_alv8_0ff. N(1)-C(1)-C(2)-O(1) -65.54(19) N(1)-C(1)-C(2)-C(3) 174.14(15) O(1)-C(2)-C(3)-N(2) 55.83(19) C(1)-C(2)-C(3)-N(2) 178.12(15) O(2)-C(4)-N(1)-C(1) 178.96(15) O(3)-C(4)-N(1)-C(1) -1.9(3) C(2)-C(1)-N(1)-C(4) -100.2(2) Symmetry transformations used to generate equivalent atoms: Table E.60: Hydrogen bonds for 8m_alv8_0ff [? and ?]. D-H...A d(D-H) d(H...A) d(D...A) <(DHA) O(1)-H(1O)...O(4)#1 1.03(4) 1.74(4) 2.7620(17) 178(3) N(2)-H(2N)...O(3)#2 0.93(2) 1.86(2) 2.7867(19) 172.9(18) N(2)-H(3N)...O(2)#3 0.90(3) 1.90(3) 2.790(2) 172(2) N(2)-H(4N)...O(2)#4 0.88(2) 1.92(2) 2.782(2) 168.2(19) O(4)-H(2O)...O(3)#5 0.90(2) 1.79(2) 2.6837(15) 171(2) O(5)-H(4O)...O(3) 0.85(2) 1.90(2) 2.7482(17) 174(2) Symmetry transformations used to generate equivalent atoms: #1 x+1,y+1,z #2 x,-y+1,z-1/2 #3 -x+2,y,-z+1/2 #4 x,-y+2,z-1/2 #5 x-1,y,z