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Molecular dynamics (MD) simulation allows one to predict the time evolution of a system of interacting particles. It is widely used in physics, chemistry and biology to address specific questions about the structural properties and dynamical mechanisms of model systems. MD earned a great success in genome research, as it proved to be beneficial in sorting pathogenic from neutral genomic mutations. Considering their computational requirements, simulations are commonly performed on HPC computing devices, which are generally expensive and hard to administer. However, variables like the software tool used for modeling and simulation or the size of the molecule under investigation might make one hardware type or configuration more advantageous than another or even make the commodity hardware definitely suitable for MD studies. This work aims to shed lights on this aspect.

The effect of ions on the structure of liquid water is still not completely understood, despite extensive experimental and theoretical studies. A combined XANES and molecular dynamics investigation on diluted Zn(2+) and Hg(2+) aqueous solutions reveals that the influence of a single ion on the bonding pattern of water molecules is strongly dependent on the nature of the ion. While the structure of water is not altered by the presence of the Zn(2+) ion, the Hg(2+) cation has a strong impact on the hydrogen-bond network of water that extends beyond the first coordination shell.

The low-lying valence electronic excitations of the topotecan anticancer drug, in two stable lactone forms, have been addressed in infinite dilute aqueous solution by combining time-dependent density functional theory calculations with nanoseconds time-scale classical molecular dynamics simulations at 298 K. The effects of the surrounding and fluctuating classical environment on the investigated topotecan forms are included in a perturbed electronic Hamiltonian, which is computed, and then diagonalized, at each frame stored during the molecular dynamics sampling in explicit solution. Current results clearly indicate that, at moderately acidic and physiological conditions, the valence UV-vis absorption spectra of topotecan drug are strongly affected by the surrounding dielectric media and by its perturbing trajectory as arising from finite-temperature fluctuations and supramolecular interactions. Furthermore, the extension of the proposed computational study to hydrated topotecan complexes in liquid water shows that all of the experimentally detected UV-vis spectroscopic features in solution are accurately reproduced only when direct solute-solvent intermolecular interactions are also explicitly taken into account in our simulating scenario. Finally, the present investigation opens up a chance regarding the computational prediction of the UV-vis absorption spectra of topotecan interacting, in silico, with the topoisomerase-DNA binary complex in physiological conditions (i.e., water dilute solution, room temperature).

A molecular mechanics (MM) force field has been developed for the topotecan (TPT) molecule, an anticancer drug the only molecular target of which is the human topoisomerase I-DNA covalent complex. We proceeded according to the amber03 force field parametrization protocol, based on quantum mechanical calculations with solvent effects included by means of continuum models. An adequate description of the electronic states of TPT has been ensured comparing calculated IR vibrational frequencies and NMR chemical shifts with experimental results. Bonded molecular parameters have been verified by comparison with ab initio normal mode vibrational analysis, while atomic charges have been fitted either using the restrained electrostatic potential fitting (RESP) or the multi-conformational RESP (MultiRESP) procedures. Particular attention has been paid to the parametrization of the dimethylamino group in ring A, for which several energy minima were found. The reliability of the force field has been checked comparing the results obtained from a classical molecular dynamics simulation with quantum mechanics ab initio energy calculations. The development of the topotecan force field makes it possible to carry out reliable simulations of the topotecan–topoisomerase–DNA ternary complex, thus allowing the investigation of important biological questions, such as the selective resistance to topotecan caused by single residue topoisomerase I mutations.

This is the first systematic study exploring the potentiality of the X-ray absorption near edge structure (XANES) technique as a structural tool for systems containing lanthanoid(III) ions. A quantitative analysis of the XANES spectra at the K- and L(3)-edges has been carried out for three hydrated lanthanoid(III) ions, namely, Yb, Nd, and Gd, in aqueous solution and in the isostructural trifluoromethanesulfonate salts. The structural and dynamic properties of the hydrated lanthanoid(III) ions in aqueous solution have been investigated by a combined experimental-theoretical approach employing X-ray absorption spectroscopy and molecular dynamics (MD) simulations. This method allows one to perform a quantitative analysis of the XANES spectra of ionic solutions using a proper description of the thermal and structural fluctuations. XANES spectra have been computed starting from the MD trajectory, without carrying out any minimization in the structural parameter space. A comparative K- and L(3)-edge XANES data analysis is presented, demonstrating the clear advantages of the L(3)-edge XANES analysis over the K-edge studies for structural investigations of lanthanoid compounds. The second hydration shells provide a detectable contribution to the L(3)-edge spectra while the K-edge data are insensitive to the more distant coordination spheres because of the strong damping and broadening of the signal caused by the extremely large core hole widths. The XANES technique has been found to be a new valuable tool for the structural characterization of metal complexes both in the solid and in the liquid state, especially in the presence of low symmetry.

The flexible nature of the first hydration shell of the cadmium(II) ion has been definitively assessed through an extensive study, combining X-ray absorption near-edge structure (XANES) spectroscopy and molecular dynamics (MD) simulations. The structural and dynamic properties of the cadmium(II) hydration shell have been determined from long-time MD simulations, and the influence of water-water interactions has been evaluated using the SPC/E and TIP5P water models. Comparison of the theoretical results with EXAFS data suggests that the TIP5P simulation provides a better description of the cadmium(II) hydration properties. XANES spectra have been computed starting from MD trajectories, without carrying out any minimization in the structural parameter space. The octahedral solvation of cadmium(II) in aqueous solution cannot be reconciled with the XANES results, while a flexible hydration shell is fully consistent with the experimental data, which unambiguously show the presence of a dominant percentage of heptahydrated species.

A detailed investigation of the hydration structure of Zn2+, Ni2+, and Co2+ in water solutions has been carried out combining X-ray absorption fine structure (EXAFS) spectroscopy and Molecular Dynamics (MD) simulations. The first quantitative analysis of EXAFS from hydrogen atoms in 3d transition metal ions in aqueous solutions has been carried out and the ion-hydrogen interactions have been found to provide a detectable contribution to the EXAFS spectra. An accurate determination of the structural parameters associated with the first hydration shell has been performed and compared with previous experimental results. No evidence of significant contributions from the second hydration shell to the EXAFS signal has been found for these solutions, while the inclusion of the hydrogen signal has been found to be important in performing a quantitative analysis of the experimental data. The high-frequency contribution present in the EXAFS spectra has been found to be due to multiple scattering (MS) effects inside the ion-oxygen first coordination shell. MD has been used to generate three-body distribution functions from which a reliable analysis of the MS contributions to the EXAFS spectra of these systems has been carried out.

Structural modifications of the Zn2+ hydration properties under high pressure (up to 2.85 GPa) have been investigated by Molecular Dynamics (MD) simulations and the first shell structural results have been experimentally validated by X-ray Absorption spectroscopy. The first shell hydration complex of the Zn2+ ion retains an octahedral symmetry with a shortening of the Zn-O distance up to 0.04 A and an increase of the thermal motion. The structural transformations occurring to water with increasing density are also investigated by MD simulations; the effect of pressure is to increase the number of interstitial water molecules, while the tetrahedral first shell cluster is only slightly distorted in the high-density conditions.