Study on conformational search of new thiosemicarbazone reagent and complexes with metal ions integrating semi-empirical quantum and molecular mechanics calculation and Monte Carlo simulation

In this study, the conformational analysis of the ML2 complexes of new thiosemicarbazone reagents with metal cations Cd2+, Ni2+, Cu2+, Hg2+, Pb2+, Mn2+ and Zn2+ is to find the conformations with the most suitable energy of the whole molecular system. The search method incorporates MM+ and PM3 calculations with Monte Carlo techniques using the Metropolis algorithm in terms of T = 298K to 473K. The initial selection conformation was done randomly after 15 repeatable conformations and 30 conformations rejected. The conformations are chosen to change by changing the torsional-dihedral angle at the position of the metal cation associated with the donor atoms N and S of thiosemicarbazone reagents. The search method is performed by random changes of the dihedral angles to create new structures and then minimize the energy for each of these angles using molecular mechanics. The unique low energy suitability is stored while high or duplicate energy structures are discarded.

Assessing Configurational Sampling in the Quantum Mechanics/Molecular Mechanics Calculation of Temoporfin Absorption Spectrum and Triplet Density of States

The absorption properties of Temoporfin, a second-generation photosensitizer employed in photodynamic therapy, are calculated with an electrostatic-embedding quantum mechanics/molecular mechanics (QM/MM) scheme in methanol. The suitability of several ensembles of geometries generated by different sampling techniques, namely classical-molecular-dynamics (MD) and QM/MM-MD thermal sampling, Wigner quantum sampling and a hybrid protocol, which combines the thermal and quantum approaches, is assessed. It is found that a QM description of the chromophore during the sampling is needed in order to achieve a good agreement with respect to the experimental spectrum. Such a good agreement is obtained with both QM/MM-MD and Wigner samplings, demonstrating that a proper description of the anharmonic motions of the chromophore is not relevant in the computation of the absorption properties. In addition, it is also found that solvent organization is a rather fast process and a long sampling is not required. Finally, it is also demonstrated that the same exchange-correlation functional should be employed in the sampling and in the computation of the excited states properties to avoid unphysical triplet states with relative energies close or below 0 eV.

Terpenoids as Renewable Nano-Sized Building Blocks

Terpenoids are a large and structurally group of natural products containing multiple five carbon containing isoprene units. Previously we have reported that irrespective of their acyclic or alicyclic nature, all the triterpenoids containing 30C’s have nano-metric lengths. In the current studies, detailed computations have been carried out with 120 naturally occurring mono- (C10), sesqui- (C15), di- (C20), sester- (C25), sesqua- (C35) and tetra- (C40) terpenoids using Gaussian 09 software with Gauss view 07 and molecular mechanics calculation using Serena software. The heat of formation and the calculated molecular lengths obtained by the two methods were compared. Interestingly, monoterpenoid to tetraterpenoid all the terpenoids (except three monoterpenoid and one sesqui-terpenoid) have molecular lengths above one nanometer making them useful as nano-sized building blocks.