Giacomo Prampolini

Integrated computational approaches for spectroscopic studies of molecular systems in the gas phase and in solution: pyrimidine as a test case

An integrated computational approach built on quantum mechanical (QM) methods, purposely tailored inter- and intra-molecular force fields and continuum solvent models combined with time-independent and time-dependent schemes to account for nuclear motion effects is applied to the spectroscopic investigation of pyrimidine in the gas phase as well as in aqueous and CCl4 solutions. Accurate post-Hartree–Fock methodologies are employed to compute molecular structure, harmonic vibrational frequencies, energies and oscillator strengths for electronic transitions in order to validate the accuracy of approaches rooted into density functional theory with emphasis also on hybrid QM/QM′ models. Within the time-independent approaches, IR spectra are computed including anharmonicities through perturbative corrections while UV–vis line-shapes are simulated accounting for the vibrational structure; in both cases, the environmental effects are described by continuum models. The effects of conformational flexibility, including solvent dynamics, are described through time-dependent models based on purposely DFT-tailored force fields applied to molecular dynamics simulations and on QM computations of spectroscopic properties. Such procedures are exploited to simulate IR and UV–vis spectra of pyrimidine in the gas phase and in solutions, leading in all cases to good agreement with experimental observations and allowing to dissect different effects underlying spectral phenomena.

JOYCE and ULYSSES: integrated and user-friendly tools for the parameterization of intramolecular force fields from quantum mechanical data

The Joyce program is augmented with several new features, including the user friendly Ulysses GUI, the possibility of complete excited state parameterization and a more flexible treatment of the force field electrostatic terms. A first validation is achieved by successfully comparing results obtained with Joyce2.0 to literature ones, obtained for the same set of benchmark molecules. The parameterization protocol is also applied to two other larger molecules, namely nicotine and a coumarin based dye. In the former case, the parameterized force field is employed in molecular dynamics simulations of solvated nicotine, and the solute conformational distribution at room temperature is discussed. Force fields parameterized with Joyce2.0, for both the dyes ground and first excited electronic states, are validated through the calculation of absorption and emission vertical energies with molecular mechanics optimized structures. Finally, the newly implemented procedure to handle polarizable force fields is discussed and applied to the pyrimidine molecule as a test case.

Calculation of the intermolecular energy of large molecules by a fragmentation scheme: Application to the 4-n-pentyl-4′- cyanobiphenyl (5CB) dimer

We present a method for computing intermolecular energies of large molecules based on a suitable fragmentation scheme, which allows one to express the complete interaction energy as a sum of interaction energies between pairs of fragments. The main advantage consists in the possibility of using standard ab initio quantum methods to evaluate the fragment energies. For the 4-n-pentyl-4′-cyanobiphenyl (5CB) dimer, the present results indicate that the most favorite arrangement corresponds to an antiparallel side-by-side geometry with a stabilization energy of about 16 kcal/mol. It is shown that, by the present method, the interaction energy of the 5CB dimer can be evaluated for all geometrical conformations and, in principle, it can be used for bulk simulations.

Absorption and emission spectra of fluorescent silica nanoparticles from TD-DFT/MM/PCM calculations

A multi-scale computational protocol, which combines Quantum Mechanics and Molecular Mechanics (QM/MM) calculations with the polarisable continuum model (PCM), has been used to study the tetramethylrhodamine isothiocyanate (TRITC) fluorophore, embedded in three different environments, namely in water, on an amorphous silica surface and covalently encapsulated in a silica nanoparticle (C dot). Absorption and emission spectra have been simulated by using TD-B3LYP/PCM calculations, performed on the TRITC ground and excited state geometries, optimized at the QM/MM level. The results are in good agreement with experimental data confirming the caging effect played by the silica shell on the mobility of the TRITC molecule when covalently encapsulated in silica nanoparticles. This could result in a decrease of the nonradiative decay rate and thus an increase of the quantum yield of the molecule.

An Integrated Protocol for the Accurate Calculation of Magnetic Interactions in Organic Magnets

A new, fast, and efficient computational protocol for the accurate calculation of singlet-triplet magnetic splittings in organic diradicals is tested and validated. This procedure essentially consists of three steps: the adoption of modified virtual orbitals (MVO) and a mixed variational-perturbational approach (CSPA) are now combined with a third method that exploits the reduction of the configurational space dimensions achieved by fragmentation/localization criteria. This innovative approach is successfully tested on four different substituted m-phenylene bis(tert-butyl) nitroxides, which show paramagnetic behavior, by computing singlet-triplet energy gaps and comparing them with their experimental counterparts.

Modeling Solvent Broadening on the Vibronic Spectra of a Series of Coumarin Dyes. From Implicit to Explicit Solvent Models.

We present a protocol to estimate the solvent-induced broadening of electronic spectra based on a model that explicitly takes into account the environment embedding the solute. Starting from a classical approximation of the solvent contribution to the spectrum, the broadening arises from the spread of the excitation energies due to the fluctuation of the solvent coordinates, and it is represented as a Gaussian line shape that convolutes the vibronic spectrum of the solute. The latter is computed in harmonic approximation at room temperature with a time-dependent approach. The proposed protocol for the computation of spectral broadening exploits molecular dynamics (MD) simulations performed on the solute-solvent system, keeping the solute degrees of freedom frozen, followed by the computation of the excitation properties with a quantum mechanics/molecular mechanics (QM/MM) approach. The factors that might influence each step of the protocol are analyzed in detail, including the selection of the empirical force field (FF) adopted in the MD simulations and the QM/MM partition of the system to compute the excitation energies. The procedure is applied to a family of coumarin dyes, and the results are compared with experiments and with the predictions of a very recent work (Cerezo et al., Phys. Chem. Chem. Phys. 2015, 17, 11401-11411), where an implicit model was adopted for the solvent. The final spectra of the considered coumarins were obtained without including ad hoc phenomenological parameters and indicate that the broadenings computed with explicit and implicit models both follow the experimental trend, increasing as the polarity change from the initial to the final state increases. More in detail, the implicit model provides larger estimations of the broadening that are closer to the experimental evidence, while explicit models appear to better capture relative differences arising from different solvents or different solutes. Possible inaccuracies of the adopted FF that may lead to the observed underestimation are analyzed in detail.

Structure and Dynamics of Ferrocyanide and Ferricyanide Anions in Water and Heavy Water: An Insight by MD Simulations and 2D IR Spectroscopy

Combined computational and experimental techniques were employed to investigate at the microscopic level the structural and dynamic properties of ferro- and ferricyanide ions in aqueous solution. The characterization of the structural patterns and multiscale dynamics taking place within the first solvation spheres in water and heavy water solvents was first achieved through extensive molecular dynamics simulations, performed with refined force fields, specifically parametrized for the cyanide ions under investigation. The information gained about the solute-solvent interactions is then validated through the successful comparison of computed and measured waiting-time-dependent 2D IR spectra. The vibrational patterns resulting from 2D IR measurements were rationalized in terms of the interaction between the ion and the neighboring water molecules described by simulation. It was found that, within the first solvation sphere, the stronger interactions of the solvent with the ferro species are responsible for a delay in the relaxation dynamics, which becomes more and more evident on longer time scales.

An automated approach for the parameterization of accurate intermolecular force-fields. Pyridine as a case study

An automated protocol is proposed and validated, which integrates accurate quantum mechanical calculations with classical numerical simulations. Intermolecular force fields, (FF) suitable for molecular dynamics (MD) and Monte Carlo simulations, are parameterized through a novel iterative approach, fully based on quantum mechanical data, which has been automated and coded into the PICKY software, here presented. The whole procedure is tested and validated for pyridine, whose bulk phase, described through MD simulations performed with the specifically parameterized FF, is characterized by computing several of its thermodynamic, structural, and transport properties, comparing them with their experimental counterparts.

Force-field modeling through quantum mechanical calculations: molecular dynamics simulations of a nematogenic molecule in its condensed phases.

Interaction energy of the 4‐n‐pentyloxy‐4′‐cyanobiphenyl (5OCB) dimer is computed at MP2 level, for many geometrical arrangements using the Fragmentation Reconstruction Method (FRM). DFT calculations are performed for a number of geometries of the monomer. The resulting database is used to parameterize an atomistic intra‐ and inter‐molecular force‐field suitable for classical bulk simulations. Several structural and dynamical properties in 5OCB isotropic and liquid crystalline phases are computed from molecular dynamics simulation mainly in the NPT ensemble. Lengthy runs (more than 70 ns) and large sample sizes (up to 806 molecules) were used to determine the nematic to isotropic transition temperature up to a precision of few K. Good agreement was found in most of the investigated properties, thus validating the accuracy of the proposed model potential, only derived by quantum mechanical calculations.

Structure-Properties Relationships in Triplet Ground State Organic Diradicals: A Computational Study.

A fast and efficient computational protocol, devised for the accurate calculation of singlet-triplet magnetic splittings in organic diradicals, is here applied to several promising organic magnets, recently considered in the literature. The very good agreement with the measured values, obtained for all investigated compounds, suggests that the present approach could successfully flank the experiment in the design of novel magnetic materials. Indeed, some structure-magnetic properties relationships were rationalized thanks to the theoretical soundness of the adopted multireference approach. In particular the different effects of N· and NO· magnetic moieties, as well as the role of lateral aliphatic chains and phenyl pendant substituents, are discussed in detail.