Perturbative multireference configuration interaction (CI-MRPT2) calculations in a focused dynamical approach: A computational study of solvatochromism in pyrimidine

We have investigated solvatochromic effects over a solvent series of increasing polarity on the prototype molecule pyrimidine as a solute species. The line shape profiles, obtained by a time-dependent approach based on quantum mechanical calculations performed over frames sampled from classical molecular dynamics trajectories, were directly compared to the available experimental bands. The multireference configuration interaction second-order perturbation (CI-MRPT2) calculations are in quantitative agreement with the experiment. The results also confirm how nonprotic solvents can be confidently modeled by continuous solvation models as the polarizable continuum model, whereas protic solvents, as water, require the inclusion of explicit solvent molecules to account for the effects of hydrogen bonds

Predicting light absorption properties of anthocyanidins in solution: a multi-level computational approach

A multi-level computational protocol is devised to calculate the absorption spectra in ethanol solution of a series of anthocyanidins relevant for dye-sensitized solar cells. The protocol exploits the high accuracy of second-order multi-reference perturbation theory to correct the results of the more feasible TD-DFT calculations, which were performed on hundreds of configurations sampled from molecular dynamics (MD) trajectories. The latter were purposely carried out with accurate and reliable force fields, specifically parameterized against quantum mechanical data, for each of the investigated dyes. Besides yielding maximum absorption wavelengths very close to the experimental values, the present approach was also capable of predicting reliable band shapes, even accounting for the subtle differences observed along the homolog series. Finally, the atomistic description achieved by MD simulations allowed for a deep insight into the different micro-solvation patterns around each anthocyanidin and their effects on the resulting dye’s properties. This work can be considered as a step toward the implementation of a computational protocol able to simulate the whole system formed by the organic dye and its heterogeneous embedding that constitutes dye-sensitized solar cells

Developing accurate intramolecular force fields for conjugated systems through explicit coupling terms

The accuracy of molecular mechanics force fields (FF) reveals critical for applications where precise molecular structures along a conformational sampling are required, as in the simulation of electronic spectroscopies. This implies abandoning generalized FFs in favor of specific FFs, with non-transferable parameters able to accurately describe the targeted species. A promising strategy in this direction consists in the so-called quantum mechanically derived FFs, in which the parameters are fitted onto reference data computed through quantum chemistry. However, in order to obtain a global set of parameters able to reliably describe the reference potential energy surface in different regions of the conformational space, the complexity of the analytical expressions of the FF becomes crucial. Regarding intramolecular interactions, the functional form of standard transferable FFs is restricted to terms that depend on only one internal coordinate. It will be shown that such models may reveal insufficient to describe systems as polyenic chains, where complex electronic effects, e.g., conjugation, intrinsically couple different internal coordinates (ICs). We propose a functional form for intramolecular FFs, which includes explicit couplings between flexible dihedrals and stiff ICs (bonds and angles), being able to properly describe the geometrical changes arising not only from steric interactions, but also from conjugation effects, i.e., the change of bond orders induced by conformational changes. The parameterization of the coupled FFs is carried out by means of automated and efficient computational protocols, purposely developed in the present work. All procedures are tested and validated by generating FFs for the two smallest compounds in the polyenic series (butadiene and hexatriene)

The phenoxyl group-modulated interplay of cation-π and σ-type interactions in the alkali metal series.

An extensive exploration of the interaction PESs of phenol and catechol complexes with alkali metal cations reveals a striking effect of –OH substitution on the balance between cation-π and σ-type noncovalent interactions

Intermolecular interactions in eumelanins: A computational bottom-up approach. I. small building blocks

The non-covalent interactions between pairs of the smallest eumelanins building blocks, 5,6-dihydroxy-indole (DHI) and its redox derivatives, are subjected to a systematic theoretical investigation, elucidating their nature and commenting on some of their possible effects on the layered structure of eumelanin. An accurate yet feasible protocol, based on second order perturbation theory, was set up and validated herein, and thereafter used to sample the intermolecular potential energy surfaces of several DHI related dimers. From the analysis of the resulting local minima, the crucial role of stacking interactions is assessed, evidencing strong effects on the geometrical arrangement of the dimer. Furthermore, the absorption spectra of the considered dimers in their most stable arrangements are computed and discussed in relation to the well known eumelanin broadband features. The present findings may help in elucidating several eumelanin features, supporting the recently proposed geometrical order/disorder model (Chen et al., Nat. Commun. 2014, 5, 3859)

Accuracy of quantum mechanically derived force-fields parameterized from dispersion-corrected DFT data: the benzene dimer as a prototype for aromatic interactions

A multilevel approach is presented to assess the ability of several popular dispersion corrected density functionals (M06-2X, CAM-B3LYP-D3, BLYP-D3, and B3LYP-D3) to reliably describe two-body interaction potential energy surfaces (IPESs). To this end, the automated Picky procedure (Cacelli et al. J. Comput. Chem. 2012, 33, 1055) was exploited, which consists in parametrizing specific intermolecular force fields through an iterative approach, based on the comparison with quantum mechanical data. For each of the tested functionals, the resulting force field was employed in classical Monte Carlo and Molecular Dynamics simulations, performed on systems of up to 1000 molecules in ambient conditions, to calculate a number of condensed phase properties. The comparison of the resulting structural and dynamic properties with experimental data allows us to assess the quality of each IPES and, consequently, even the quality of the DFT functionals. The methodology is tested on the benzene dimer, commonly used as a benchmark molecule, a prototype of aromatic interactions. The best results were obtained with the CAM-B3LYP-D3 functional. Besides assessing the reliability of DFT functionals in describing aromatic IPESs, this work provides a further step toward a robust protocol for the derivation of sound force field parameters from quantum mechanical data. This method can be relevant in all those cases where standard force fields fail in giving accurate predictions

Magnetic gaps in organic tri-radicals: From a simple model to accurate estimates

The calculation of the energy gap between the magnetic states of organic poly-radicals still represents a challenging playground for quantum chemistry, and high-level techniques are required to obtain accurate estimates. On these grounds, the aim of the present study is twofold. From the one side, it shows that, thanks to recent algorithmic and technical improvements, we are able to compute reliable quantum mechanical results for the systems of current fundamental and technological interest. From the other side, proper parameterization of a simple Hubbard Hamiltonian allows for a sound rationalization of magnetic gaps in terms of basic physical effects, unraveling the role played by electron delocalization, Coulomb repulsion, and effective exchange in tuning the magnetic character of the ground state. As case studies, we have chosen three prototypical organic tri-radicals, namely, 1,3,5-trimethylenebenzene, 1,3,5-tridehydrobenzene, and 1,2,3-tridehydrobenzene, which differ either for geometric or electronic structure. After discussing the differences among the three species and their consequences on the magnetic properties in terms of the simple model mentioned above, accurate and reliable values for the energy gap between the lowest quartet and doublet states are computed by means of the so-called difference dedicated configuration interaction (DDCI) technique, and the final results are discussed and compared to both available experimental and computational estimates

Quantitative prediction and interpretation of spin energy gaps in polyradicals: the virtual magnetic balance

Open-shell organic molecules possessing more than two unpaired electrons and sufficient stability even at room temperature are very unusual, but few were recently synthesized that promise a number of fascinating applications. Unfortunately, reliable structural information is not available and only lower limits can be estimated for energy splittings between the different spin states. On these grounds, we introduce here an effective ‘virtual magnetic balance’, a robust and user-friendly tool purposely tailored for polyradicals and devised to be used in parallel with experimental studies. The main objective of this tool is to provide reliable structures and quantitative splittings of spin states of large, complex molecules. We achieved this objective with reasonable computation times and in a theoretical framework that allows disentanglement of different stereo-electronic effects contributing to the overall experimental result. A recently synthesized tetraradical with remarkable chemical stability was used as a case study

Noncovalent Interactions in the Catechol Dimer

Noncovalent interactions play a significant role in a wide variety of biological processes and bio-inspired species. It is, therefore, important to have at hand suitable computational methods for their investigation. In this paper, we report on the contribution of dispersion and hydrogen bonds in both stacked and T-shaped catechol dimers, with the aim of delineating the respective role of these classes of interactions in determining the most stable structure. By using second-order Møller–Plesset (MP2) calculations with a small basis set, specifically optimized for these species, we have explored a number of significant sections of the interaction potential energy surface and found the most stable structures for the dimer, in good agreement with the highly accurate, but computationally more expensive coupled cluster single and double excitation and the perturbative triples (CCSD(T))/CBS) method

Adiabatic-Molecular Dynamics Generalized Vertical Hessian Approach: A Mixed Quantum Classical Method to Compute Electronic Spectra of Flexible Molecules in the Condensed Phase

We present a general mixed quantum classical method that couples classical molecular dynamics (MD) and vibronic models to compute the shape of electronic spectra of flexible molecules in the condensed phase without, in principle, any phenomenological broadening. It is based on a partition of the nuclear motions of the solute + solvent system in "soft" and "stiff" vibrational modes and an adiabatic hypothesis that assumes that stiff modes are much faster than soft ones. In this framework, the spectrum is rigorously expressed as a conformational integral of quantum vibronic spectra along the stiff coordinates only. Soft modes enter at the classical level through the conformational distribution that is sampled with classical MD runs. In each configuration, reduced-dimensionality quadratic Hamiltonians are built in the space of the stiff coordinates only, thanks to a generalization of the Vertical Hessian harmonic model and an iterative application of projectors in internal coordinates to remove soft modes. Quantum vibronic spectra, specific for each sampled configuration of the soft coordinates, are then computed at the desired temperature with efficient time-dependent techniques, and the global spectrum simply arises from their average. For consistency of the whole procedure, classical MD runs are performed with quantum-mechanically derived force fields, parameterized at the same level of theory selected for generating the quadratic Hamiltonians along the stiff coordinates. Application to N-methyl-6-oxyquinolinium betaine in water, dithiophene in ethanol, and cyanidine in water is presented to show the performance of the methodThis work has received funding from the European Union’s Horizon 2020 research and innovation programme MSCA-ITN under grant agreement no. 765266 (LightDyNAmics). Computational resources provided by the Centro de Cálculo Científico at Universidad Autónoma de Madrid (CCC-UAM) and by SCBI (Supercomputing and Bioinformatics) center of Universidad de Málaga are also acknowledged. D.A. and F.A. acknowledge financial support from Spanish “Ministerio de Economía y Competitividad” (project CTQ2015-65816-R). D.A. acknowledges Fundación Ramón Areces (Spain) for funding his postdoctoral stay at ICCOM-CNR Pisa. J.C. and D.A. acknowledge the Pisa Unit of ICCOM-CNR for hospitality