(a) The titin-I27 domain highlighting the disulfide bridging bond and a schematic representation of the stretching of the polyprotein strain by the aid of the atomic force microscopy; (b) the titin- model, designed to model the redox-active site in the titin-I27 domain, created from one snapshot (Ref. 58) of titin-I27 during a molecular-dynamics simulation of the force induced unfolding.
Timings at the BP86/6- level of theory for a single construction of the XC and the density-fitted-Coulomb contribution to the Kohn–Sham matrix as a function of the number of carbon atoms for linear polyene chains . The Coulomb timings are separated into timings for the near-field contribution (NF-J), the far-field contributions (FF-J), and the linear equation solver (Linsol). The auxiliary basis set in Ref. 59 was used as the density-fitting basis.
Timings at the BP86/6- level of theory for the calculation of the molecular gradient as a function of the number of carbon atoms for linear polyene chains . Timings are for the non-Coulomb one-electron contribution (1el), the XC contribution, and the (one- and two-electron) near-field (NF-J) and far-field (FF-J) Coulomb contributions to the gradient. The auxiliary basis set in Ref. 59 was used as the density-fitting basis.
Timings in seconds for a single construction of the Kohn–Sham matrix and for the calculation of the molecular gradient for a range of molecules, ordered by increasing number of atoms (Atoms), at the BP86 level of theory. The timings are split into contributions from the XC and the density-fitted NF and FF Coulomb contributions. For the force evaluation, we also give the one-electron kinetic-energy and reorthonormalization contribution (1el). Also listed are the number of primitive (Prim) and contracted (Cont) basis functions. The auxiliary basis set in Ref. 59 was used in all cases, except otherwise stated.
Average timings in seconds for the electronic energy, the molecular gradient, and the geometry step for the geometry optimizations of the taxol, valinomycin, and titin-. All calculations were carried out at the BP86/6-31G level of theory with the auxiliary basis set in Ref. 59. Also reported are the average number of SCF iterations in each energy optimization, with the root-mean-square SCF gradient norm converged to , and the number of geometry steps needed to converge the geometry, with threshold (see text).
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