Molecular mechanics modeling of organic backbone of metal-free and coordinated ligands

Synthesis and Structural Properties of Patellamide A Derivatives and Their Copper(ii) Compounds

“…Conformational analyses were performed with the MOMEC 97 [39] program and force field, [21,36,40] using the random kick stochastic searching module. [36] To scan the conformational space in each structure, six individual structures were generated based on the EPR simulation parameters.…”

“…15 ± 30 structures for each of the species analyzed), [21,40] and the EPR simulation with the structural parameter sets obtained from each of the lowest energy optimized structures. The molecular mechanical structure optimization is based on harmonic bonding potentials and, therefore, the coordination number is fixed, while the coordination geometry is flexible, due to the replacement in MOMEC of the harmonic valence angle bending potentials by 1,3-nonbonded interactions around the metal center.…”

“…These might be the results of ambiguities in the measurement of the geometric parameters from the strain-energy-minimized structures [21,40] (see above), small inconsistencies in the force field used, the neglect of solvation, and some inconsistencies in the EPR spectral simulations might also contribute to the limited accuracy. The structural results are listed in Table 3 …”

Evaluations of AMBER force field parameters by MINA approach for copper-based nucleases

“…More interestingly, the difference ranges of some compounds with same or similar ligands are very close, even though those compounds may belong to different types. Similarly, the ranges for the copper nucleases in A1-bpy/dione/dpq/dppz are comparable with the previously reported results [22,29,[114][115][116].…”

“…This could be related to the five-membered ring of Cu1-N2-N3-C8-C9, together with the two aromatic rings in bpy group, resulting more stable for the rigid aromatic part, so when changing the angle (Cu1-N2-C8/Cu1-N3-C9) within the rigid 5-membered ring, the effect of the N^O ligand at the other side of copper center should be less. But for the remaining bond and angle, the values of these parameters appear to be more random, i.e., the ranges of 81-108, 67-100, 124-144 kcal mol -1 Å -2 for bonds Cu1-N2, Cu1-N5 and Cu1-O4, which are mostly in the reported ranges of 59-204, 33-242, 36-250 kcal mol -1 -rad -2 [22,29,[114][115][116], and the ranges of 81-106, 81-103, 49-72 kcal mol -1 rad -2 for angles Cu1-N3-C7, Cu1-O4-C10 and N3-Cu1-O4 in A1-/A2-/A3-/A4-bpy, respectively. Especially for A2-bpy, the differences for bond parameters are large than those of other structures, for example, the parameter for Cu1-N2/Cu1-N3/Cu1-N5 is 107 Å -2 in A4-bpy, which may be caused by the long polar group (-CH 2 CH 2 CH 2 CH 2 NH 3 ) in A2-bpy.…”