An integrated computational protocol for the accurate prediction of EPR and PNMR parameters of aminoxyl radicals in solution

Magnetic spectroscopic techniques such as electron paramagnetic resonance (EPR) and paramagnetic NMR (PNMR) are valuable tools for understanding the structure and dynamics of complex systems such as, for example, biomolecules or nanomaterials labeled with suitable free radicals. Unfortunately, such spectra do not give direct access to the radical structure because of the subtle interplay between several different effects not easily separable and evaluable by experimentalists alone. In this respect, computational spectroscopy is becoming an essential and versatile tool for the assignment and interpretation of experimental spectra. In this article, the new integrated computational approaches developed in the recent years in our research group are reviewed. Such approaches have been applied to two widely used spin probes showing that proper account of stereo-electronic, environmental and dynamical effects leads to magnetic properties in remarkable agreement with experimental results.

Environmental effects in computational spectroscopy: accuracy and interpretation

Spectroscopic techniques are valuable tools for understanding the structure and dynamics of complex systems, such as biomolecules or nanomaterials. Most of the current research is devoted to the development of new experimental techniques for improving the intrinsic resolution of different spectra. However, the subtle interplay of several different effects acting at different length and time scales still makes the interpretation and analysis of such spectra a very difficult task. In this respect, computational spectroscopy is becoming a needful and versatile tool for the assignment and interpretation of experimental spectra. It is in fact possible nowadays to model with relatively high accuracy the physical-chemical properties of complex molecules in different environments, and to link spectroscopic evidence directly to the structural and dynamical properties of optically or magnetically active solvated probes. In this Review, significant steps toward the simulation of entire spectra in condensed phases are presented together with some basic aspects of computational spectroscopy, which highlight how intramolecular and intermolecular degrees of freedom influence several spectroscopic parameters.

Simulating DNA hybridization on an amine-functionalized silicon substrate

The ability of DNA biosensors to capture oligonucleotide molecules in solution is of great importance in genetics, medical diagnostics, and drug discovery. The DNA hybridization event in which the probe, which is usually a single-stranded DNA segment covalently immobilized on a functionalized surface via a cross-linker molecule, recognizes the complementary target and forms a stable duplex structure is the basis of highly specific biorecognizing devices. The rate of hybridization depends on the solvent, length of the strands, complexity of the system, and other factors and could be considerably altered by the type of attachment and by the density of the probe on the substrates. Recent experimental investigations have shown that some probes can hybridize directly from bulk solutions. In this computational study, we provide a model for the behavior of these systems choosing cross-linker, probe, and target on the basis of experimental data. MD simulations of the single-stranded DNA fragment 5'-d(TGGC)-3' attached to an allylamine-functionalized Si(111) surface through an oxanine cross-linker in aqueous solution containing the complementary sequence, i.e. 5'-d(CGCCA)-3', are presented. A possible probe-target capture mechanism obtained using explicit solvent and state-of-the-art classical molecular dynamics simulation protocols is described. The hybridization process of the tethered DNA single strand, the intermediate structures appeared during the formation of the double helix, their internal dynamics and their behavior with respect to the substrate are characterized in detail.

Harmonic and Anharmonic Vibrational Frequency Calculations with the Double-Hybrid B2PLYP Method: Analytic Second Derivatives and Benchmark Studies

This work aims to provide reliable benchmark data on the accuracy of harmonic and anharmonic vibrational frequencies computed with the B2PLYP double-hybrid density functional method. The exchange-correlation contributions required for the B2PLYP analytical second derivatives are presented here, which allow for the effective calculation of harmonic frequency as well as cubic and semidiagonal quartic force fields. The latter, in turn, are necessary to compute the anharmonic vibrational frequencies with the perturbative approach (VPT2). The quality of harmonic vibrational frequencies computed in conjunction with basis sets of double- to quadruple-ζ quality has been checked against reference data from the F38 benchmark set. Then, for an additional set of small closed- and open-shell systems, both harmonic frequencies and anharmonic contributions computed at the B2PLYP/N07D and the B2PLYP/aug-cc-pVTZ levels have been compared to their CCSD(T) counterparts. Moreover, for selected medium-size molecules (furan, pyrrole, thiophene, uracil, anisole, phenol, and pyridine), anharmonic frequencies have been compared to well established experimental results. Such benchmark studies have shown that the B2PLYP/N07D model provides good quality harmonic frequencies and describes correctly anharmonic contributions, the latter being of similar accuracy to their B3LYP/N07D counterparts, but obtained at significantly larger computational cost. Additionally, increased accuracy can be obtained by adopting hybrid models where the B2PLYP/N07D anharmonic contributions are combined with harmonic frequencies computed with more accurate quantum mechanical (QM) approaches or by B2PLYP with larger basis sets. This work confirmed also that most of the recently developed density functionals are significantly less suited for vibrational computations, while the B2PLYP method can be recommended for spectroscopic studies where a good accuracy of vibrational properties is required.

Vibronic model for the quantum dynamical study of the competition between bright and charge-transfer excited states in single-strand polynucleotides: the adenine dimer case

A simple vibronic model aimed at investigating the interplay between bright excitonic states and dark charge-transfer (CT) states in stacked adenine (Ade) nucleobases is presented. Two orbitals (the HOMO and the LUMO) for each Ade site have been included in the electronic Hamiltonian, whose parameters have been fitted to reproduce the main features of the absorption spectra of two stacked 9-methyladenine (9Me-A) molecules, computed in aqueous solution at the PCM/TD-PBE0 level. Three modes for each adenine unit have been included in the Hamiltonian, to describe the main structural changes among the different excited state minima of the adenine stacked dimer, as described at the TD-DFT level. The developed vibronic Hamiltonian (four electronic states and six nuclear coordinates) has been adopted to perform quantum dynamical calculations of a photoexcited Ade stacked dimer, utilizing the multiconfigurational time-dependent Hartree method. The obtained results indicate that the transfer between the bright excitonic state and the CT state is fast and effective.