Automated Parameterization of Quantum Mechanically Derived Force Fields for Soft Materials and Complex Fluids: Development and Validation.

The reliability of molecular dynamics (MD) simulations in predicting macroscopic properties of complex fluids and soft materials, such as liquid crystals, colloidal suspensions, or polymers, relies on the accuracy of the adopted force field (FF). We present an automated protocol to derive specific and accurate FFs, fully based on ab initio quantum mechanical (QM) data. The integration of the Joyce and Picky procedures, recently proposed by our group to provide an accurate description of simple liquids, is here extended to larger molecules, capable of exhibiting more complex fluid phases. While the standard Joyce protocol is employed to parameterize the intramolecular FF term, a new automated procedure is here proposed to handle the computational cost of the QM calculations required for the parameterization of the intermolecular FF term. The latter is thus obtained by integrating the old Picky procedure with a fragmentation reconstruction method (FRM) that allows for a reliable, yet computationally feasible sampling of the intermolecular energy surface at the QM level. The whole FF parameterization protocol is tested on a benchmark liquid crystal, and the performances of the resulting quantum mechanically derived (QMD) FF were compared with those delivered by a general-purpose, transferable one, and by the third, "hybrid" FF, where only the bonded terms were refined against QM data. Lengthy atomistic MD simulations are carried out with each FF on extended 5CB systems in both isotropic and nematic phases, eventually validating the proposed protocol by comparing the resulting macroscopic properties with other computational models and with experiments. The QMD-FF yields the best performances, reproducing both phases in the correct range of temperatures and well describing their structure, dynamics, and thermodynamic properties, thus providing a clear protocol that may be explored to predict such properties on other complex fluids or soft materials.

Accurate interaction energies by spin component scaled Möller-Plesset second order perturbation theory calculations with optimized basis sets (SCS-MP2mod): Development and application to aromatic heterocycles.

The Spin Component Scaled (SCS) MP2 method using a reduced and optimized basis set (SCS-MP2mod) is employed to compute the interaction energies of nine homodimers, formed by aromatic heterocyclic molecules (pyrrole, furan, thiophene, oxazole, isoxazole, pyridine, pyridazine, pyrimidine, and pyrazine). The coefficients of the same-spin and opposite-spin correlation energies and the Gaussian type orbitals (GTO) polarization exponents of the 6-31G** basis set are simultaneously optimized in order to minimize the energy differences with respect to the coupled-cluster with single, double and perturbative triples excitations [CCSD(T)] reference interaction energies, extrapolated to a complete basis set. It is demonstrated that the optimization of the spin scale factors leads to a noticeable improvement of the accuracy with a root mean square deviation less than 0.1 kcal/mol and a largest unsigned deviation smaller than 0.25 kcal/mol. The pyrrole dimer provides an exception, with a slightly higher deviation from the reference data. Given the high benefit in terms of computational time with respect to the CCSD(T) technique and the small loss of accuracy, the SCS-MP2mod method appears to be particularly suitable for extensive sampling of intermolecular potential energy surfaces at a quantum mechanical level. Within this framework, a transferability test of the SCS-MP2mod parameters to a benchmark set of this class of molecules is very promising as the reference interaction energies of several heterocyclic aromatic heterodimers were reproduced with a standard deviation of 0.30 kcal/mol. The SCS-MP2mod remarkably outperforms the value of 1.95 kcal/mol obtained with standard MP2/6-31G**.

A General Treatment to Study Molecular Complexes Stabilized by Hydrogen-, Halogen-, and Carbon-Bond Networks: Experiment and Theory of (CH2 F2 )n ⋠⋠⋠(H2 O)m.

Rotational spectra of several difluoromethane-water adducts have been observed using two broadband chirped-pulse Fourier-transform microwave (CP-FTMW) spectrometers. The experimental structures of (CH2 F2 )⋅⋅⋅(H2 O)2 , (CH2 F2 )2 ⋅⋅⋅(H2 O), (CH2 F2 )⋅⋅⋅(H2 O)3 , and (CH2 F2 )2 ⋅⋅⋅(H2 O)2 were unambiguously identified with the aid of 18 isotopic substituted species. A subtle competition between hydrogen, halogen, and carbon bonds is observed and a detailed analysis was performed on the complex network of non-covalent interactions which stabilize each cluster. The study shows that the combination of stabilizing contact networks is able to reinforce the interaction strength through a cooperative effect, which can lead to large stable oligomers.

Development and Validation of Quantum Mechanically Derived Force-Fields: Thermodynamic, Structural, and Vibrational Properties of Aromatic Heterocycles.

A selection of several aromatic molecules, representative of the important class of heterocyclic compounds, has been considered for testing and validating an automated Force Field (FF) parametrization protocol, based only on Quantum Mechanical data. The parametrization is carried out separately for the intra- and intermolecular contributions, employing respectively the Joyce and Picky software packages, previously implemented and refined in our research group. The whole approach is here automated and integrated with a computationally effective yet accurate method, devised very recently ( J. Chem. THEORY: Comput., 2018, 14, 543-556) to evaluate a large number of dimer interaction energies. The resulting quantum mechanically derived FFs are then used in extensive molecular dynamics simulations, in order to evaluate a number of thermodynamic, structural, and dynamic properties of the heterocycle's gas and liquid phases. The comparison with the available experimental data is good and furnishes a validation of the presented approach, which can be confidently exploited for the design of novel and more complex materials.

The role of the multiconfigurational character of nitronyl-nitroxide in the singlet-triplet energy gap of its diradicals.

While technological applications demand the development of reliable computational techniques and accurate experiments for the characterization of diradicals, these species are still challenging systems for both theory and experiments. The singlet-triplet energy gap, the J-term of the Heisenberg-Dirac-van Vleck spin Hamiltonian, is the most significant quantity; its measurement and computational evaluation may serve for understanding and controlling magnetism at the molecular scale. In this framework, we report a study of three diradicals containing one or two nitronyl-nitroxide species. Using Difference Dedicated Configuration Interaction (DDCI) calculations, we investigate the multiconfigurational character of the O-N-C-N-O fragment of this unit. We find that a computational scheme that takes this nature into account is necessary to confidently obtain reliable values of the spin-spin coupling J. In addition, we show that the reduced DDCI2 scheme with a CAS(2,2) reference, which can reproduce experimental data in some cases, provides quite poor results in the present context.

Interaction Energy Landscapes of Aromatic Heterocycles through a Reliable yet Affordable Computational Approach.

Noncovalent interactions between homodimers of several aromatic heterocycles (pyrrole, furan, thiophene, pyridine, pyridazine, pyrimidine, and pyrazine) are investigated at the ab initio level, employing the Möller-Plesset second-order perturbation theory, coupled with small Gaussian basis sets (6-31G* and 6-31G**) with specifically tuned polarization exponents. The latter are modified using a systematic and automated procedure, the MP2mod approach, based on a comparison with high level CCSD(T) calculations extrapolated to a complete basis set. The MP2mod results achieved with the modified 6-31G** basis set show an excellent agreement with CCSD(T)/CBS reference energies, with a standard deviation less than 0.3 kcal/mol. Exploiting its low computational cost, the MP2mod approach is then used to explore sections of the intermolecular energy of the considered homodimers, with the aim of rationalizing the results. It is found that the direct electrostatic interaction between the monomers electron clouds is at the origin of some observed features, and in many cases multipoles higher than dipole play a relevant role, although often the interplay with other contributions to the noncovalent forces (as for instance induction, π-π or XH-π interactions) makes a simple rationalization rather difficult.

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.

Eumelanin broadband absorption develops from aggregation-modulated chromophore interactions under structural and redox control.

Eumelanins, the chief photoprotective pigments in man and mammals, owe their black color to an unusual broadband absorption spectrum whose origin is still a conundrum. Excitonic effects from the interplay of geometric order and disorder in 5,6-dihydroxyindole (DHI)-based oligomeric/polymeric structures play a central role, however the contributions of structural (scaffold-controlled) and redox (π-electron-controlled) disorder have remained uncharted. Herein, we report an integrated experimental-theoretical entry to eumelanin chromophore dynamics based on poly(vinyl alcohol)-controlled polymerization of a large set of 5,6-dihydroxyindoles and related dimers. The results a) uncover the impact of the structural scaffold on eumelanin optical properties, disproving the widespread assumption of a universal monotonic chromophore; b) delineate eumelanin chromophore buildup as a three-step dynamic process involving the rapid generation of oxidized oligomers, termed melanochromes (phase I), followed by a slow oxidant-independent band broadening (phase II) leading eventually to scattering (phase III); c) point to a slow reorganization-stabilization of melanochromes via intermolecular redox interactions as the main determinant of visible broadband absorption.

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.

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.

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.

BALOO: A Fast and Versatile Code for Accurate Multireference Variational/Perturbative Calculations.

We present the new BALOO package for performing multireference variational/perturbative computations for medium- to large-size systems. To this end we have introduced a number of conceptual and technical improvements including full parallelization of the code, use and manipulation of a large panel of reference orbitals, implementation of diagrammatic perturbation treatment, and computation of properties by density matrix perturbed to the first-order. A number of test cases are analyzed with special reference to electronic transitions and magnetic properties to show the versatility, effectiveness, and accuracy of BALOO.

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.

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.

Electron transport properties of diarylethene photoswitches by a simplified NEGF-DFT approach.

A homemade program called FOXY has been used for the theoretical investigation on the conducting properties of two diarylethene based molecules, which, according to recent literature data, can act as photoswitches. FOXY uses a simplified method relying on NEGF theory coupled to DFT calculations and using a suitable electric field to mimic the bias voltage, together with a simple representation of the electrodes. The results confirm the experimental findings and are rationalized by analyzing the space extension of the pertinent molecular orbitals in the ON and OFF electronic states and confirm the FOXY program as a cheap and reliable code to be used in the field of molecular electronics.

Computational Screening of Weak Hydrogen Bond Networks: Predicting Stable Structures for Difluoromethane Oligomers.

The stability and the structure of small difluoromethane oligomers are studied by combining classical Monte Carlo and quantum mechanical calculations. A hierarchical procedure was adopted to validate the accuracy of the whole protocol: the force field used in Monte Carlo simulations is parametrized on the basis of dimer intermolecular energies computed with density functional theory. The density functional is similarly chosen by comparing the interaction energies with reference values, purposely computed at a coupled cluster level, extrapolated at the complete basis set. The structures of dimers, trimers, and tetramers identified by the screening as local minima are first characterized by some geometrical parameters and by their dipole moment and eventually validated by comparison with results of microwave spectroscopy. The results are found in very good agreement with the experiment for all considered structures.

Proton and Electron Transfer Mechanisms in the Formation of Neutral and Charged Quinhydrone-Like Complexes: A Multilayered Computational Study.

The redox and proton transfer processes involving the several dimers arising from quinones are studied by quantum mechanical methods using second order perturbation theory (MP2) and a medium size basis set optimized for reproducing dispersion interactions. Furthermore, bulk solvent effects are taken into account by the polarizable continuum solvent (PCM) approach possibly integrated by two explicit water molecules for an improved description of the cybotactic region. Our results indicate that several neutral and anionic dimers are kept together mainly by strong hydrogen bonds, but dispersion forces introduce additional non-negligible effects. The computed energy paths indicate that a proton transfer process should accompany the two-electron reduction of quinhydrone and that two dimers in the reduced form can be simultaneously present in solution, in agreement with available experimental data.

Oligomers based on weak hydrogen bond networks: a rotational study of the tetramer of difluoromethane.

We report the rotational spectrum of one conformer of the tetramer of difluoromethane (CH2F2)4 (the first pure rotational spectrum of a tetramer of an asymmetric rotor), and describe the network of weak hydrogen bonds which connect the four subunits.

Transport properties of binuclear metal complexes of the VIII group using a simplified NEGF-DFT approach.

We report on a theoretical study of the electronic transport properties of binuclear complexes of metals of the VIII group bridged by pyrazine. Metal-porphyrazine units have been combined in order to investigate symmetric and non-symmetric species with particular focus on their current rectification properties. Transmission functions and I-V characteristics of the various species have been computed using a Non-Equilibrium Green Function with a simplified treatment of the molecule-lead interaction. The results obtained show an overall moderate asymmetry in the current along the molecules, which is of the donor-σ-acceptor type and follow the trend of the ionization potential of the metals in the binuclear system. The bias-dependent rectification ratio, which is significant in a limited voltage window, can be explained in terms of the alignment of the occupied orbitals of the metallic fragments that contribute to the HOMO and HOMO - 1 of the supermolecule. The possible improvement of the rectification performance of such a class of molecules has also been investigated exploiting suitable substitution by electron-withdrawing groups.