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.

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

CAS(2,2) reference may not be sufficient for the computation of singlet–triplet energy gap by DDCI.

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.

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.

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 at room temperature are very unusual, but some of them were recently synthesized and promise a number of fascinating applications.

Parametrization and Validation of Intramolecular Force Fields Derived from DFT Calculations

The energy and its first and second geometrical derivatives obtained by DFT calculations for a number of conformations of a single molecule are used to parametrize intramolecular force fields, suitable for computer simulations. A systematic procedure is proposed to adequately treat either fully atomistic or more simplified force fields, as within the united atom approach or other coarse grained models. The proposed method is tested and validated by performing molecular dynamics simulations on several different molecules, comparing the results with literature force fields and relevant experimental data. Particular emphasis is given to the united atom approach for flexible molecules characterized by "soft" torsional potentials which are known to retain a high degree of chemical specificity.

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

Building eumelanin: from basic units to spectral properties.

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.

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.

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 dye's 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.

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.

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.

Theoretical Study of the Photochemical Isomerization of Colchicine

The photochemical reaction of colchicine to β- and γ-lumicolchicine, through a mechanism involving a disrotatory cyclization, is studied by theoretical methods. The energetics of the reaction, including one or two methanol solvent molecules, are studied at the DFT-B3LYP and multireference perturbation levels of theory using the 6-31G(d) basis set. The results show that, in agreement with experimental results, the first excited state of colchicine at ∼3.6 eV can lead to both β- and γ-lumicolchicine, whose energy is about 15 kcal mol(-)(1) above the colchicine energy. Owing to the high steric tension of the condensed four- and five-atom rings arising from cyclization, the two trans-lumicolchicines are higher in energy (>60 kcal mol(-)(1)), and their formation appears much less probable. A partial inclusion of the solvent effects through the addition of two solvent molecules does not alter the general conclusions based on the free energy in the gas phase. The photochemical reaction path is studied by choosing the distance between the two carbon atoms which form the new σ bond as the leading coordinate of the minimum-energy path of both the ground and the first singlet excited states. The energies are computed by Multi Configurational self-consistent-field calculations on a model molecule, retaining those atoms that presumably play an active role in the reaction. A reasonable mechanism starting from colchicine in the first singlet excited state and leading to γ-lumicolchicine is proposed. On the contrary, a high-energy transition state is found for trans-lumicolchicines, whose formation, although not strictly forbidden for energetic reasons, appears to be rather improbable.

Liquid Crystal Properties of the n-Alkyl-cyanobiphenyl Series from Atomistic Simulations with Ab Initio Derived Force Fields

Lengthy molecular dynamics (MD) simulations were performed at constant atmospheric pressure and different temperatures for the series of the 4-n-alkyl-4'-cyanobiphenyls (nCB) with n = 6, 7, and 8. The accurate atomistic force field (Bizzarri, M.; Cacelli, I.; Prampolini, G; Tani, A. J. Phys. Chem. A 2004, 108, 10336), successfully employed to reproduce thermodynamic and transport properties of the 5CB molecule, has here been extended to higher homologues. Nematic and isotropic phases were found for all members of the series, and also, a smectic phase was (tentatively) identified for 8CB at 1 atm and 300 K. Transition temperatures reproduce the experimental values within +/-10 K. Also, structural properties as second and fourth rank orientational order parameters are in good agreement with the corresponding experimental quantities. This means that the well-known odd-even effect, observed for many properties along the nCB series, is well reproduced, despite the narrow range of oscillations, e.g., in clearing temperatures. A detailed analysis of the correlation between molecular properties and odd-even effects is presented.