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

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)

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

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)

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

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

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

A density functional study of open-shell cyclopentadienyl-molybdenum(II) complexes. A comparison of stabilizing factors: Spin-pairing, Mo-X π bonding, and release of steric pressure

The dissociation of PH3 from the 18-electron system CpMoX(PH3)3 to afford the corresponding 16-electron CpMoX(PH3)2 fragment has been investigated theoretically by density functional theory for X = H, CH3, F, Cl, Br, I, OH, and PH2. The product is found to prefer a triplet spin state for all X ligands except PH2, the singlet-triplet gap varying between 1.7 kcal/mol for OH to 8.7 kcal/mol for F. The Mo-PH3 bond dissociation energy to the 16-electron ground state varies dramatically across the series, from 4.5 kcal/mol for OH to 23.5 kcal/mol for H, and correlates with experimental observations on trisubstituted phosphine derivatives. Geometry-optimized spin doublet CpMo(PH3)3, on the other hand, has a Mo-PH3 bond dissociation energy of 24.3 kcal/mol. The modulation of the Mo-PH3 bond dissociation energy by the introduction of X is analyzed in terms of three effects that stabilize the 16-electron product relative to the 18-electron starting complex: (i) adoption of the higher (triplet) spin state by release of pairing energy; (ii) Mo-X π interactions; (iii) release of steric pressure. A computational model for the approximate separation and evaluation of these three stabilizing effects is presented. According to the results of these calculations, the relative importance of the three effects depends on various factors related to the nature of X. For double-sided π-donor X ligands, the larger triplet-singlet gap is provided by the more electronegative atoms (F \u3e CL \u3e Br \u3e I), whereas single-sided π donors favor the singlet state. The π-stabilization ability goes in the order PH2 \u3e OH \u3e F \u3e other halogens \u3e H. Finally, the major steric interaction appears to be associated with the presence of inactive lone pairs and by their orientation/proximity to the PH3 ligands (Cl, Br \u3e I, OH \u3e F, PH2, H, CH3). The 16-electron methyl system establishes a marked α-agostic interaction in the singlet state, which nevertheless remains unfavored relative to an undistorted triplet configuration

Systematic and Automated Development of Quantum Mechanically Derived Force Fields: The Challenging Case of Halogenated Hydrocarbons

A robust and automated protocol for the derivation of sound force field parameters, suitable for condensed-phase classical simulations, is here tested and validated on several halogenated hydrocarbons, a class of compounds for which standard force fields have often been reported to deliver rather inaccurate performances. The major strength of the proposed protocol is that all of the parameters are derived only from first principles because all of the information required is retrieved from quantum mechanical data, purposely computed for the investigated molecule. This a priori parametrization is carried out separately for the intra- and intermolecular contributions to the force fields, respectively exploiting the Joyce and Picky programs, previously developed in our group. To avoid high computational costs, all quantum mechanical calculations were performed exploiting the density functional theory. Because the choice of the functional is known to be crucial for the description of the intermolecular interactions, a specific procedure is proposed, which allows for a reliable benchmark of different functionals against higher-level data. The intramolecular and intermolecular contribution are eventually joined together, and the resulting quantum mechanically derived force field is thereafter employed in lengthy molecular dynamics simulations to compute several thermodynamic properties that characterize the resulting bulk phase. The accuracy of the proposed parametrization protocol is finally validated by comparing the computed macroscopic observables with the available experimental counterparts. It is found that, on average, the proposed approach is capable of yielding a consistent description of the investigated set, often outperforming the literature standard force fields, or at least delivering results of similar accuracy